{"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A chicken Fab, Cy.004, targeting the Cysteine-rich protective antigen (CyRPA) of Plasmodium falciparum. CyRPA is essential for the invasion of host erythrocytes by blood stage merozoites and is required for assembly of the PfRH5 adhesion complex at the merozoite-erythrocyte interface. The antibody is designed to inhibit parasite growth by binding to blades 1 and 2 of the CyRPA \u03b2-propeller, with binding mediated by calcium coordination at the antibody-antigen interface.", "target_protein": "AVTLDESGGGLQTPGGALSLVCKASMGWVRQAPGKGLEYVAGLYTPAVKGRATISRDNGQSTVRLQLNNLRAEDTATYFCWGHGTEVIVSSAGFDFSSYAIRNDGSFTTKSADDGGHYSDFSGEIDA", "metadata": {"pdb_id": "7phw", "light_chain_seq": "LTQPSSVSANPGETVKITCSGSTYNYGWYQQKSPGSAPVTVIYYNDKRPSDIPSRFSGSKSGSTGTLTITGVQAEDEAVYYCGNSDSRNVAFGAGTTLTVLRT", "cdrh1_seq": "GFDFSSYA", "cdrh2_seq": "IRNDGSFT", "cdrh3_seq": "TKSADDGGHYSDFSGEIDA", "cdrl1_seq": "TYNY", "cdrl2_seq": "YND", "cdrl3_seq": "GNSDSRNVA", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[22, 25]", "cdrl2_pos": "[43, 45]", "cdrl3_pos": "[82, 90]", "cdrh3_split": "val", "cdrh3_cluster": "7phw", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Cy.004", "antibody_format": "Fab", "heavy_subclass": "unknown", "light_subclass": "unknown", "is_engineered": false, "target_antigen": "Cysteine-rich protective antigen, Plasmodium falciparum", "target_domain": null, "functional_role": "other", "evidence_quote": "growth inhibitory antibody that inhibits parasite growth"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 11218, 6914, 16, 6002, 18, 11373, 16, 5133, 1920, 8666, 17, 5536, 6337, 4730, 12, 6002, 11119, 1019, 13, 1927, 15663, 13098, 18, 6002, 11119, 1019, 1977, 4415, 1958, 1920, 6254, 1927, 4423, 14161, 2007, 2877, 3587, 6902, 21831, 1930, 1977, 3414, 1958, 5957, 1927, 1920, 5099, 5004, 1015, 6141, 2796, 2019, 1920, 6902, 26553, 17, 15469, 6854, 18, 1920, 3533, 1977, 4609, 1942, 2875, 8652, 2905, 2007, 2743, 1942, 22707, 1036, 21, 1930, 22, 1927, 1920, 6002, 11119, 1019, 161, 17, 5062, 13728, 16, 1956, 2743, 3434, 2007, 5016, 9478, 2019, 1920, 3533, 17, 4730, 6854, 18, 3], "antigen": ["RHVFIRTELSFIKNNVPCIRDMFFIYKRELYNICLDDLETHIYVQKKVKDSWITLNDLFKETDLTGRPHIFAYVDVEEIIILLCEDEEFSNRKKDMTCHRFYSNDGKEYNNAEITISDYILKDKLLSSYVSLPLKIENREYFLICGVSPDDILCMASHDKGETWGTKIVIKYDNYKLGVQYFFLRPYISKNDLSFHFYVGDNIVKNVNFIECTHEKDLEFVCSNRDFLKDNKVLQDVSTLNDEYIVSYGNDNNFAECYIFFNNENSILIKPEKYGGCYGGTFVKIDENRALFIYSSSQGIYNIHTIYYANYE"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A murine Fab, mAb 5-6 (IGHV5/IGKV17-Kappa), targeting the engineered Neuraminidase Ind11 of Influenza A virus. Neuraminidase catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates, cleaving sialic acids during virus budding and spread to prevent self-aggregation and ensure efficient cell-to-cell transmission. The antibody is designed as a neutralizing antibody targeting the active site of neuraminidase, binding within the Head of neuraminidase, to inhibit viral replication and confer protection against Ind11 H3N2 infection. Please output the HCDRs.", "target_protein": "EVQLVESGGDLVKPGGSLKLSCAASMSWVRQTPDKRLEWVATYYPDSVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCWGTGTPVTVSSGFTFSSYGISSGGSYTARGGYYGSSYWYFDV", "metadata": {"pdb_id": "9md2", "light_chain_seq": "ETTVTQSPASLSMAVGKKVTIRCITSTGVDDDMNWYQQKPGEPPKLLISEGNTLRPGVPSRFSSSGYGTDFVFTIENMLSEDVADYYCLQSDNLPYTFGGGTKLEIK", "cdrh1_seq": "GFTFSSYG", "cdrh2_seq": "ISSGGSYT", "cdrh3_seq": "ARGGYYGSSYWYFDV", "cdrl1_seq": "TGVDDD", "cdrl2_seq": "EGN", "cdrl3_seq": "LQSDNLPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "1xiw", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "5-6", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV17", "is_engineered": true, "target_antigen": "Neuraminidase Ind11, Influenza A virus", "target_domain": "Head of neuraminidase", "functional_role": "neutralizing", "evidence_quote": "inhibit viral replication in vivo; protection from infection in mice"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 7032, 25, 17, 26, 12, 20733, 1020, 1015, 19, 7021, 1040, 7390, 1027, 17, 12093, 13, 16, 5133, 1920, 11091, 29831, 2063, 3242, 1927, 7108, 43, 3413, 18, 29831, 17097, 1920, 6025, 1927, 4262, 20436, 2687, 4248, 2037, 4324, 1930, 3689, 4235, 30378, 2209, 16, 28634, 20436, 4576, 2409, 3413, 15909, 1930, 6441, 1942, 4625, 3543, 17, 7883, 1930, 6486, 5807, 2024, 17, 1942, 17, 2024, 5303, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 3500, 3200, 1927, 29831, 16, 2743, 2651, 1920, 4469, 1927, 29831, 16, 1942, 2875, 4324, 5158, 1930, 7909, 6202, 3316, 2063, 3242, 25234, 2909, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["GEYRNWSKPQCNITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNGHSNNTVHDRTPYRTLLMNELGVPFHLGTRQVCMAWSSSSCHDGKAWLHVCITGNDNNATASFIYNGRLVDSIGSWSKNILRTQESECVCINGTCTVVMTDGSASGKADTKILFVEEGKIVHISTLSGSAQHVEECSCYPRFPGVRCVCRDNWKGSNRPIVDINVKNYSIVSSYVCSGLVGDTPRKSDSVSSSYCLDPNNEKGGHGVKGWAFDDGNDVWMGRTINETLRLGYETFKVIEGWSKANSKLQTNRQVIVEKGDRSGYSGIFSVEGKSCINRCFYVELIRGRKEETKVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab, S1V2-72 (IGHV1/IGLV2-Lambda), targeting the Hemagglutinin of Influenza B virus (B/Malaysia/2506/2004). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and is responsible for penetration of the virus into the cell cytoplasm by mediating fusion of the viral and endosomal membranes. The antibody is designed to recognize a conserved epitope preferentially exposed in the postfusion conformation of influenza A and B hemagglutinins, providing protection against lethal infection through Fc\u03b3 receptor-dependent mechanisms including ADCC.", "target_protein": "QVQLVQSGAELKKPGASVKVSCKASIHWMRQVPGQGLEWMGWHHAQKFQGRVDMTRDTSINTAYLELTRLESDDTALYYCWGQGTLVTVSSAGYTFTGNYINPRTGDTARCVFATSQFDP", "metadata": {"pdb_id": "8udg", "light_chain_seq": "QSALTQPASVSGSPGQSITISCTGTNSDIGSHNLVSWYQQHPGKAPKVMIYDDSKRPSGVSNRFSGSKSGSTASLTISGLQSEDEADYYCCSYAGSSNWVFGGGTKLTLLAA", "cdrh1_seq": "GYTFTGNY", "cdrh2_seq": "INPRTGDT", "cdrh3_seq": "ARCVFATSQFDP", "cdrl1_seq": "NSDIGSHNL", "cdrl2_seq": "DDS", "cdrl3_seq": "CSYAGSSNWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[25, 33]", "cdrl2_pos": "[51, 53]", "cdrl3_pos": "[90, 99]", "cdrh3_split": "val", "cdrh3_cluster": "8udg", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S1V2-72", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza B virus (B/Malaysia/2506/2004)", "target_domain": null, "functional_role": "other", "evidence_quote": "protects against lethal IAV and IBV infections via Fc\u03b3 receptor\u2013dependent mechanisms"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 16, 4062, 15755, 17, 4395, 12, 20733, 7390, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 26141, 1927, 7108, 44, 3413, 12, 44, 19, 21720, 19, 6330, 1016, 19, 4247, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 1977, 5061, 1958, 12006, 1927, 1920, 3413, 2460, 1920, 2024, 5239, 2007, 10239, 5289, 1927, 1920, 4324, 1930, 16514, 5726, 18, 1920, 3533, 1977, 4609, 1942, 9967, 43, 5305, 10095, 10662, 4616, 1922, 1920, 2753, 9049, 7748, 1927, 7108, 43, 1930, 44, 26141, 1036, 16, 5453, 6202, 3316, 10470, 2909, 2596, 17536, 3148, 17, 3100, 3531, 2710, 25899, 18, 3], "antigen": ["GYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDEIHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVDIGNGCFETKHKCNQTCLDRIAAGTFNAGEFSLPTFDSLNITAASLNDDG"]} {"modality_type": "antibody", "text": "Output the HCDRs for an antibody that performs this function: A human Fab, S2L20 (IGHV3/IGKV1-Kappa), targeting the N-terminal domain (NTD) of the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes through conformational changes and proteolytic cleavage. The antibody is designed to function as a membrane-anchored receptor capable of promoting SARS-CoV-2 entry through NTD-mediated mechanisms that induce RBD opening and exposure of the S2' cleavage site for fusion activation.", "target_protein": "EVQLVESGGGVVQPGGSLRLSCAASMHWVRQAPGKGLEWVAFYYADSVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCWGQGTLVTVSGFTFNSYGIRYDGGNKANLKDSRYSGSYYDY", "metadata": {"pdb_id": "9c44", "light_chain_seq": "VIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKVDFK", "cdrh1_seq": "GFTFNSYG", "cdrh2_seq": "IRYDGGNK", "cdrh3_seq": "ANLKDSRYSGSYYDY", "cdrl1_seq": "QDIRFY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYDNLPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9c44", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S2L20", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "N-terminal domain (NTD)", "functional_role": "other", "evidence_quote": "S2L20-CVR acts as a functional receptor for SARS-CoV-2, supporting membrane fusion, pseudovirus entry, and authentic virus infection"}}}, "tokenized_instruction": [2, 6647, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 17436, 2052, 2347, 30, 43, 2616, 6914, 16, 5159, 11232, 1008, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 56, 17, 4262, 3418, 12, 22078, 13, 1927, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 1930, 12712, 6404, 18, 1920, 3533, 1977, 4609, 1942, 2347, 1966, 43, 3260, 17, 17199, 3148, 7131, 1927, 7356, 20466, 17, 6083, 17, 22, 6904, 2596, 22078, 17, 3434, 3531, 1988, 4769, 25780, 9497, 1930, 3395, 1927, 1920, 5159, 11, 6404, 3200, 1958, 5289, 2936, 18, 3], "antigen": ["QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHSWMESEFRVYSSANNCTFEYVSQPFLFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPEL"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A murine Fab (IGHV1/IGKV10-Kappa) targeting an engineered fusion construct of the D(2) dopamine receptor with soluble cytochrome b562 (N- to C-terminus). The D(2) dopamine receptor is a GPCR that mediates dopamine signaling through G-protein-coupled inhibition of adenylyl cyclase. This antibody is intended as a structural tool to stabilize the D(2) dopamine receptor for crystallographic studies, binding at the extracellular region to enable structure determination of the receptor in complex with ligands.", "target_protein": "EVQLQQSGAELVKPGASVKISCKASMNWVKQSRGKSLEWIGYNYNQRFKGKATLTVDKSSSTAYIQLNSLTSEDSAVYYCWGQGTSVTVSSAGYSFTGYNINPFYGTTARRYLTGTGAMDY", "metadata": {"pdb_id": "7dfp", "light_chain_seq": "DIVMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLLYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEPEDIATYYCQQYSKLPRTFGGGTKLEIKRA", "cdrh1_seq": "GYSFTGYN", "cdrh2_seq": "INPFYGTT", "cdrh3_seq": "ARRYLTGTGAMDY", "cdrl1_seq": "QDISNY", "cdrl2_seq": "YTS", "cdrl3_seq": "QQYSKLPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7dfp", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV10", "is_engineered": false, "target_antigen": "D(2) dopamine receptor fused to soluble cytochrome b562", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "antibody recognizing the D2R structure (IgG3089) and prepared a novel Fab fragment (Fab3089)"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 1008, 17, 12093, 13, 5133, 1925, 11091, 5289, 6377, 1927, 1920, 46, 12, 22, 13, 7964, 3148, 1956, 6622, 9387, 24365, 8166, 12, 56, 17, 1942, 45, 17, 7822, 13, 18, 1920, 46, 12, 22, 13, 7964, 3148, 1977, 43, 12542, 1988, 10412, 7964, 3197, 2596, 49, 17, 2213, 17, 6416, 3523, 1927, 27802, 16526, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 1920, 46, 12, 22, 13, 7964, 3148, 1958, 17832, 2351, 16, 2743, 2019, 1920, 5329, 3031, 1942, 8675, 3170, 7063, 1927, 1920, 3148, 1922, 2796, 1956, 6908, 18, 3], "antigen": ["NYYATLLTLLIAVIVFGNVLVCMAVSREKALQTTTNYLIVSLAVADLLVATLVMPWVVYLEVVGEWKFSRIHCDIFVTLDVMMCTAKIWNLCAISIDRYTAVAMPMSKRRVTVMISIVWVLSFTISCPLLFGLNNADQNECIIANPAFVVYSSIVSFYVPFIVTLLVYIKIYIVLLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAGSDILVGQIDDALKLANEGKVKEAQAAAEQLKTTINAYIQKYGSQQKEKKATQMLAIVLGVFIICWLPFFITHILNIHCDCNIPPVLYSAFTWLGYVNSAVNPIIYTTFNIEFRKAFLKILH"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A human Fab, ZK2B10 (IGHV1/IGLV1-Lambda), targeting the ZIKV structural E protein of Zika virus. The E protein is the envelope glycoprotein that mediates viral entry and fusion. The antibody is designed as a neutralizing antibody that protects against ZIKV infection by blocking steps between fusion intermediate formation and membrane fusion, binding within DIII.", "target_protein": "EVQLVQSGAEVKKPGASVKVSCKASINWVRQATGQGLEWMGWGYAQKFQGRVTMTRNTSINTAYMELSSLRSEDTAVYYCWGQGTTVTVSSAGYTFTSGHTFPSYDMNPNRGNTARVRSGTNYGSYYYYYYGMDV", "metadata": {"pdb_id": "6jfh", "light_chain_seq": "SYELTQPPSASGTPGQRVTISCSGSSSNIGNNYVHWYQQLPGSAPKLLIYRNNQRPSGVPDRFSGSKSGTSGSLAISGLRSEDEADYYCASWDDSLSGHWVFGGGTKVTVLGQ", "cdrh1_seq": "GYTFTSGHTFPSYD", "cdrh2_seq": "MNPNRGNT", "cdrh3_seq": "ARVRSGTNYGSYYYYYYGMDV", "cdrl1_seq": "SSNIGNNY", "cdrl2_seq": "RNN", "cdrl3_seq": "ASWDDSLSGHWV", "cdrh1_pos": "[25, 38]", "cdrh2_pos": "[56, 63]", "cdrh3_pos": "[102, 122]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 100]", "cdrh3_split": "val", "cdrh3_cluster": "6jfi", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ZK2B10", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "ZIKV structural E protein, Zika virus", "target_domain": "DIII", "functional_role": "neutralizing", "evidence_quote": "capable of protection against Zika virus infection and microcephaly"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 2616, 6914, 16, 68, 6779, 5090, 1008, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 17359, 4346, 47, 2213, 1927, 28593, 3413, 18, 1920, 47, 2213, 1977, 1920, 11262, 11424, 1988, 10412, 4324, 6904, 1930, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 14576, 3316, 17359, 2909, 2007, 7472, 5983, 2192, 5289, 6129, 3337, 1930, 3260, 5289, 16, 2743, 2651, 26028, 1033, 18, 3], "antigen": ["IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTA"]} {"modality_type": "antibody", "text": "A murine Fab, YN69083 (IGHV1/IGKV4-Kappa), targeting the Hepatic sodium/bile acid cotransporter (NTCP) of Homo sapiens. NTCP plays a key role in the enterohepatic circulation of bile salts necessary for the solubilization and absorption of dietary fat and fat-soluble vitamins, and acts as an entry receptor for hepatitis B virus. The antibody is intended as a structural tool to stabilize NTCP in its outward-open conformation for structural characterization. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "EVQLQQPGAELVKPGASVKLSCKTSMKWVKQRPGQGLEWIGENYNGKFKSKASLTVDKSSSTAYMQLSSLTSEDSAVYYCWGLGTSVTVSSAGYTFTNYWINPSNGGTTILVYDAYYVFAMDY", "metadata": {"pdb_id": "7fci", "light_chain_seq": "DIVMTQSPAIMSASPGQKVTITCSASSSVNYMHWYQQKLGSSPKLWIYDTSKLALGVPARFSGSGSGTSYSLTISSMEAEDAASYFCHQWSSYPRTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTNYW", "cdrh2_seq": "INPSNGGT", "cdrh3_seq": "TILVYDAYYVFAMDY", "cdrl1_seq": "SSVNY", "cdrl2_seq": "DTS", "cdrl3_seq": "HQWSSYPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "7fci", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "YN69083", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Sodium/bile acid cotransporter (NTCP), Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "Fab fragment was shown to increase the Tm of NTCP by more than 5 \u00b0C, indicating that the protein is correctly folded"}}}, "tokenized_instruction": [2, 43, 7135, 6914, 16, 67, 1022, 7093, 13895, 1010, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 16, 5133, 1920, 6095, 5227, 19, 9619, 2687, 14817, 24095, 12, 5891, 10020, 13, 1927, 16350, 27974, 18, 5891, 10020, 5705, 43, 3834, 2770, 1922, 1920, 5553, 28600, 2479, 9255, 1927, 9619, 16028, 4680, 1958, 1920, 27635, 1930, 6726, 1927, 6096, 3777, 1930, 3777, 17, 6622, 18818, 16, 1930, 8016, 1966, 1925, 6904, 3148, 1958, 7977, 44, 3413, 18, 1920, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 5891, 10020, 1922, 2496, 18411, 17, 4437, 7748, 1958, 4346, 7285, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["LPPNFGKRPTDLALSVILVFMLFFIMLSLGCTMEFSKIKAHLWKPKGLAIALVAQYGIMPLTAFVLGKVFRLKNIEALAILVCGCSPGGNLSNVFSLAMKGDMNLSIVMTTCSTFCALGMMPLLLYIYSRGIYDGDLKDKVPYKGIVISLVLVLIPCTIGIVLKSKRPQYMRYVIKGGMIIILLCSVAVTVLSAINVGKSIMFAMTPLLIATSSLMPFIGFLLGYVLSALFCLNGRCRRTVSMETGCQNVQLCSTILNVAFPPEVIGPLFFFPLLYMIFQLGEGLLLIAIFWCYEKF"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab (IGHV3/IGKV1-Kappa) targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2, specifically the B.1.617.1 (Kappa) variant. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. This antibody forms a complex with the Spike glycoprotein N-terminal domain.", "target_protein": "EVQLVESGGGVVQPGGSLRLSCAASMHWVRQAPGKGLEWVAFYYADSVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCWGQGTLVTVSGFTFNSYGIRYDGGNKANLKDSRYSGSYYDY", "metadata": {"pdb_id": "7sod", "light_chain_seq": "VIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKVDFK", "cdrh1_seq": "GFTFNSYG", "cdrh2_seq": "IRYDGGNK", "cdrh3_seq": "ANLKDSRYSGSYYDY", "cdrl1_seq": "QDIRFY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYDNLPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9c44", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "N-terminal domain (NTD)", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 16, 4475, 1920, 44, 18, 21, 18, 5473, 1027, 18, 21, 12, 12093, 13, 6031, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 11424, 56, 17, 4262, 3418, 18, 3], "antigen": ["QCVNLQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHADNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYMKSEFRVYSSANNCTFEYVSQPFLMFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSF"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab, IMC-11F8 (IGHV4/IGKV3-Kappa), targeting the engineered extracellular region of the Epidermal growth factor receptor. The Epidermal growth factor receptor is a receptor tyrosine kinase that binds ligands of the EGF family and activates multiple downstream signaling cascades including RAS-RAF-MEK-ERK, PI3 kinase-AKT, PLCgamma-PKC, and STATs pathways. The antibody is designed to inhibit EGFR signaling as an antitumor therapeutic.", "target_protein": "QVQLQESGPGLVKPSQTLSLTCTVSWSWIRQPPGKGLEWIGYDYNPSLKSRVTMSVDTSKNQFSLKVNSVTAADTAVYYCWGQGTLVTVSSAGGSISSGDYYIYYSGSTARVSIFGVGTFDY", "metadata": {"pdb_id": "3b2v", "light_chain_seq": "EIVMTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCHQYGSTPLTFGGGTKAEIKRT", "cdrh1_seq": "GGSISSGDYY", "cdrh2_seq": "IYYSGST", "cdrh3_seq": "ARVSIFGVGTFDY", "cdrl1_seq": "QSVSSY", "cdrl2_seq": "DAS", "cdrl3_seq": "HQYGSTPLT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3b2u", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "IMC-11F8", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Epidermal growth factor receptor, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "EGFR inhibition by an antibody drug IMC-11F8"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 2042, 1030, 17, 2513, 1038, 1025, 12, 20733, 1020, 1006, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 5329, 3031, 1927, 1920, 9844, 2905, 2991, 3148, 18, 1920, 9844, 2905, 2991, 3148, 1977, 43, 3148, 6941, 4016, 1988, 6876, 6908, 1927, 1920, 4451, 3416, 1930, 9094, 3137, 5863, 3197, 15967, 2710, 6520, 17, 12783, 17, 12551, 17, 7770, 16, 21197, 4016, 17, 5496, 16, 12897, 4223, 28262, 17, 8425, 16, 1930, 3156, 1036, 3873, 18, 1920, 3533, 1977, 4609, 1942, 2875, 5775, 3197, 1966, 1925, 11775, 4272, 18, 3], "antigen": ["TCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCP"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab, BA7125 (IGHV3/IGKV1-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors, initiating infection, and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a broadly neutralizing antibody against diverse SARS-CoV-2 variants, binding within the Receptor-binding domain (RBD) at the thumb region with minimal interaction with mutational residues in current variants.", "target_protein": "EVQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVAVYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTTVTVSSAGFTFSSYAISFDGSNKARASITTTDDGMDV", "metadata": {"pdb_id": "7xcz", "light_chain_seq": "DIQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPFSFGPGTKVDIKRT", "cdrh1_seq": "GFTFSSYA", "cdrh2_seq": "ISFDGSNK", "cdrh3_seq": "ARASITTTDDGMDV", "cdrl1_seq": "QGISSW", "cdrl2_seq": "AAS", "cdrl3_seq": "QQANSFPFS", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7xcz", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "BA7125", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing activity against all variants except the Omicron sublineages"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6813, 9948, 4198, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 3316, 6445, 20466, 17, 6083, 17, 22, 4936, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 2019, 1920, 22362, 3031, 1956, 6343, 2835, 1956, 13736, 4248, 1922, 3214, 4936, 18, 3], "antigen": ["TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A murine Fab, 2F2 (IGHV9/IGKV3-Kappa), targeting the JEV E protein of Japanese encephalitis virus. The JEV E protein is the surface envelope protein responsible for viral attachment and membrane fusion during entry. The antibody is designed as a neutralizing antibody that blocks receptor attachment and prevents viral fusion.", "target_protein": "QVQLMESGPELKKPGETVKISCTTSMHWVKQAPGKGLEWMGWTYAYDFKERFGFSLETSASTAFLQISNLKIEDTATYFCWGAGTSVTVSSPGYTFTDYAINTATGEPASDGRYWYFGV", "metadata": {"pdb_id": "5ywo", "light_chain_seq": "DIVLTQSPASLAVSLGQRATISCRASQSVSTSYMHWYQQKPGQPPRLLIYLVSNLESGVPSRFSGSGSGTDFTLNIHPVEAEDEATYYCQHIRELTRSEAGPSWL", "cdrh1_seq": "GYTFTDYA", "cdrh2_seq": "INTATGEP", "cdrh3_seq": "ASDGRYWYFGV", "cdrl1_seq": "QSVSTSY", "cdrl2_seq": "LVS", "cdrl3_seq": "QHIR", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 92]", "cdrh3_split": "val", "cdrh3_cluster": "5ywo", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2F2", "antibody_format": "Fab", "heavy_subclass": "IGHV9", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "JEV E protein, Japanese encephalitis virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "block attachment of the virus to its receptor and also prevent fusion of the virus"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 13775, 1028, 12, 20733, 1020, 1026, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 30173, 47, 2213, 1927, 10405, 18744, 3413, 18, 1920, 30173, 47, 2213, 1977, 1920, 3154, 11262, 2213, 5061, 1958, 4324, 8576, 1930, 3260, 5289, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 3148, 8576, 1930, 10299, 4324, 5289, 18, 3], "antigen": ["FNCLGMGNRDFIEGASGATWVDLVLEGDSCLTIMANDKPTLDVRMINIEASQLAEVRSYCYHASVTDISTVARCPMTGEAHNEKRADSSYVCKQGFTDRGWGNGCGLFGKGSIDTCAKFSCTSKAIGRTIQPENIKYEVGIFVHGTTTSENHGNYSAQVGASQAAKFTVTPNAPSITLKLGDYGEVTLDCEPRSGLNTEAFYVMTVGSKSFLVHREWFHDLALPWTPPSSTAWRNRELLMEFEEAHATKQSVVALGSQEGGLHQALAGAIVVEYSSSVKLTSGHLKCRLKMDKLALKGTTYGMCTGKFSFAKNPADTGHGTVVIELSYSGSDGPCKIPIVSVASLNDMTPVGRLVTVNPFVATSSANSKVLVEMEPPFGDSYIVVGRGDKQINHHWHKAGSTLGKAFLTTLKGAQRLAALGDTAWDFGSIGGVFNSIGKAVHQVFGGAFRTLFGGMSWITQGLMGALLLWMGVNARDRSIALAFLATGGVLLFLATNVHA"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human Fab (IGHV4/IGKV4-Kappa) targeting Activin receptor type-2B and Activin receptor type-1B, which form an activin receptor complex that transduces activin signals from the cell surface to regulate neuronal differentiation and survival, hair follicle development, FSH production, wound healing, and extracellular matrix production. The antibody is intended to stabilize the ternary signaling complex formed between the two receptors and their ligands, serving as a structural tool to visualize receptor-ligand interactions.", "target_protein": "QLQLQESGPGLVKPSETLSLTCTVSWGWIRQPPGKGLEWIGSYYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCWGQGTTVTVSSAGGSISSSSYYISYSGSTARDSLRYGMDV", "metadata": {"pdb_id": "7mrz", "light_chain_seq": "DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYALAPPRTFGGGTKVEIKRT", "cdrh1_seq": "GGSISSSSYY", "cdrh2_seq": "ISYSGST", "cdrh3_seq": "ARDSLRYGMDV", "cdrl1_seq": "QSVLYSSNNKNY", "cdrl2_seq": "WAS", "cdrl3_seq": "QQYALAPPRT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 107]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 103]", "cdrh3_split": "val", "cdrh3_cluster": "7mrz", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Activin receptor type-2B and Activin receptor type-1B, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "Anti-ActRIIB Fab fragment in ternary complex with GDF11 and receptor fusion"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1006, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 21797, 3148, 2601, 17, 5751, 1930, 21797, 3148, 2601, 17, 5462, 16, 2154, 2386, 1925, 21797, 3148, 2796, 1988, 30334, 1036, 21797, 4771, 2037, 1920, 2024, 3154, 1942, 5741, 5121, 4155, 1930, 3298, 16, 7018, 14792, 2740, 16, 13540, 3372, 16, 6376, 7872, 16, 1930, 5329, 4526, 3372, 18, 1920, 3533, 1977, 11214, 1942, 13448, 1920, 18734, 3197, 2796, 5333, 2192, 1920, 2288, 4086, 1930, 2310, 6908, 16, 13915, 1966, 43, 4346, 5229, 1942, 13159, 3148, 17, 5207, 3719, 18, 3], "antigen": ["ETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPEAGALLCACTSCLQANYTCETDGACMVSIFNLDGMEHHVATCIPKVELVPAGKPFYCLSSEDLRNTHCCYTDYCNRID"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A human Fab, MW05 (IGHV1/IGKV3-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors, initiating infection and mediating fusion of viral and cellular membranes. The antibody is designed to bind the Receptor-binding domain (RBD), recognizing an epitope that overlaps the ACE2 binding surface and capable of binding both \"up\" and \"down\" RBD conformations.", "target_protein": "EVQLVQSGAEVKKPGSSVKVSCKASISWVRQAPGQGLEWMGRNYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCWGQGTLVTVSSAGGTFSSYAIIPIFGSSAESPLGGGSGYSVSWFDP", "metadata": {"pdb_id": "7dk0", "light_chain_seq": "EIVMTQSPATLSVSPGERATLSCRASQSVSSNLAWYQQKPGQAPRLLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQYSNWPPWTFGQGTKVEIKRT", "cdrh1_seq": "GGTFSSYA", "cdrh2_seq": "IIPIFGSS", "cdrh3_seq": "AESPLGGGSGYSVSWFDP", "cdrl1_seq": "QSVSSN", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYSNWPPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "7dk0", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "MW05", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "other", "evidence_quote": "neutralizing mAb that mediates antibody-dependent enhancement (ADE) via Fc\u03b3RIIB"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 8825, 15264, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 16, 12410, 2909, 1930, 10239, 5289, 1927, 4324, 1930, 3689, 5726, 18, 1920, 3533, 1977, 4609, 1942, 4566, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 15667, 1925, 10095, 1988, 19853, 1920, 8298, 1028, 2743, 3154, 1930, 7131, 1927, 2743, 2321, 6, 2353, 6, 1930, 6, 3292, 6, 25780, 12526, 18, 3], "antigen": ["TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab, S2L20 (IGHV3/IGKV1-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (Omicron BA.5 variant). The Spike glycoprotein attaches the virion to the host cell membrane by interacting with host receptors to initiate infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody against Omicron variants, utilizing a conserved mechanism to inhibit immune escape.", "target_protein": "EVQLVESGGGVVQPGGSLRLSCAASMHWVRQAPGKGLEWVAFYYADSVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCWGQGTLVTVSGFTFNSYGIRYDGGNKANLKDSRYSGSYYDY", "metadata": {"pdb_id": "8gtq", "light_chain_seq": "VIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKVDFK", "cdrh1_seq": "GFTFNSYG", "cdrh2_seq": "IRYDGGNK", "cdrh3_seq": "ANLKDSRYSGSYYDY", "cdrl1_seq": "QDIRFY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYDNLPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9c44", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S2L20", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "antibodies could effectively inhibit the immune escape of Omicron"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 5159, 11232, 1008, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 7254, 1935, 2830, 6813, 18, 25, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1942, 11051, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 3316, 7254, 1935, 2830, 4936, 16, 10232, 43, 5305, 2856, 1942, 2875, 3743, 11781, 18, 3], "antigen": ["PPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYMESEFRVYSSANNCTFEYVSQPFLMDFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A human Fab (IGHV3/IGKV1-Kappa) targeting the engineered NS1 protein of Zika virus. NS1 is derived from the viral genome polyprotein and functions as a signal peptide for NS4B, required for interferon antagonism activity. This antibody forms a complex with NS1. Generate the corresponding HCDRs.", "target_protein": "VQLLESGGGLIQPGGSLRLSCAASMNWVRQAPGKGLEWVSIYYADSVKGRFTISRDTRKNTLYLQMHSLRVEDTAVYYCWGQGTLVTVSSGLTVSNNYIYSSGSTARERGWLDY", "metadata": {"pdb_id": "8jkf", "light_chain_seq": "IWMTQSPSSLSASVGDRVTITCRASQSVSSHLNWYQQKPGKAPKLLIYAVSSLQSGVPSRFSGGDSGTDFTLTIASLQPEDFATYYCQQTYTIPRTFGQGTKVEIK", "cdrh1_seq": "GLTVSNNY", "cdrh2_seq": "IYSSGST", "cdrh3_seq": "ARERGWLDY", "cdrl1_seq": "QSVSSH", "cdrl2_seq": "AVS", "cdrl3_seq": "QQTYTIPRT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 55]", "cdrh3_pos": "[94, 102]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "8jkf", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "NS1, Zika virus", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11091, 19082, 2213, 1927, 28593, 3413, 18, 19082, 1977, 3595, 2037, 1920, 4324, 3843, 6240, 5684, 1930, 4088, 1966, 43, 2733, 4207, 1958, 4246, 14919, 16, 3414, 1958, 10001, 18394, 2455, 18, 2052, 3533, 4952, 43, 2796, 1956, 19082, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["HHHHHGCSVDFSKKETRCGTGVFVYNDVEAWRDRYKYHPDSPRRLAAAVKQAWEDGICGISSVSRMENIMWRSVEGELNAILEENGVQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGKSYFVRAAKTNNSFVVDGDTLKECPLKHRAWNSFLVEDHGFGVFHTSVWLKVREDYSLECDPAVIGTAVKGKEAVHSDLGYWIESEKNDTWRLKRAHLIEMKTCEWPKSHTLWTDGIEESDLIIPKSLAGPLSHHNTREGYRTQMKGPWHSEELEIRFEECPGTKVHVEETCGTRGPSLRSTTASGRVIEEWCCRECTMPPLSFRAKDGCWYGMEIRPRKEPESNLVRSMVTA"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human Fab, hB9L9.3 (IGHV3/IGLV3-Lambda), targeting Frizzled-10 of Homo sapiens. Frizzled-10 is a receptor for Wnt proteins that functions in the canonical Wnt/beta-catenin signaling pathway, leading to activation of disheveled proteins, inhibition of GSK-3 kinase, nuclear accumulation of beta-catenin, and activation of Wnt target genes. The antibody is designed to modulate Wnt pathway signaling through a predefined functional site, binding within the FZ domain.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASMFWVRQAPGKGLEWVAGNYGSAVKGRATISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTFSSFNIDDDGSYPAKSGYGGSWGGYIADDIDA", "metadata": {"pdb_id": "7x8t", "light_chain_seq": "ELTQPPSVSVSPGQTARITCSGDGSYAGSYYYGWYQQKPGQAPVTLIYYNNKRPSGIPERFSGSLSGSTNTLTISGVQAEDEADYYCGSADNSGAAFGGGTKLTVLGQ", "cdrh1_seq": "GFTFSSFN", "cdrh2_seq": "IDDDGSYP", "cdrh3_seq": "AKSGYGGSWGGYIADDIDA", "cdrl1_seq": "GSYAGSYY", "cdrl2_seq": "YNN", "cdrl3_seq": "GSADNSGAA", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[23, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "7x8t", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "hB9L9.3", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "Frizzled-10, Homo sapiens", "target_domain": "FZ", "functional_role": "other", "evidence_quote": "antibodies exhibited the expected modulatory activity on the Wnt pathway"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 6914, 16, 4873, 1026, 1024, 1026, 18, 23, 12, 20733, 1020, 1010, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 5133, 9081, 18559, 2824, 17, 2119, 1927, 16350, 27974, 18, 9081, 18559, 2824, 17, 2119, 1977, 43, 3148, 1958, 7028, 2697, 1988, 4088, 1922, 1920, 9452, 7028, 19, 4666, 17, 7723, 3197, 3374, 16, 4523, 1942, 2936, 1927, 14362, 9488, 10471, 2697, 16, 3523, 1927, 9822, 17, 23, 4016, 16, 4254, 4858, 1927, 4666, 17, 7723, 16, 1930, 2936, 1927, 7028, 2758, 2628, 18, 1920, 3533, 1977, 4609, 1942, 8480, 7028, 3374, 3197, 2596, 43, 20514, 3183, 3200, 16, 2743, 2651, 1920, 17441, 3418, 18, 3], "antigen": ["KCQPIEIPMCKDIGYQMTRMPNLMGHENQREAAIQLHEFAPLVEYGCHGHLRFFLCSLYAPMCTEQVSTPIPACRVMCEQARLKCSPIMEQFNFKWPDSLDCRKLPNKNDPNYLCMEAP"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human Fab, 2-15 (IGHV1/IGLV2-Lambda), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the host cell membrane by interacting with the ACE2 receptor, initiating infection, and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody of the VH1-2 class, binding within the Receptor-binding domain (RBD) and capable of recognizing both up and down RBD conformations on the trimeric spike.", "target_protein": "VQLVQSGAEVKKPGASVRVSCKASMHWVRQAPGQGLEWMGWNYAQKFQGWVTMTRDTSISTVYMELSRLRSDDTAVYYCWGQGTMITVSSAGYTFTGYYINPISDGTARGGSRCSGGNCYGWAYDAFDI", "metadata": {"pdb_id": "7l5b", "light_chain_seq": "SALTQPASVSGSPGQSITISCTGTSSDVGGYNFVSWYQQHPGKAPKLMIYDVSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADCYCSSYTSSSTFVFGTGTKVTVLGQ", "cdrh1_seq": "GYTFTGYY", "cdrh2_seq": "INPISDGT", "cdrh3_seq": "ARGGSRCSGGNCYGWAYDAFDI", "cdrl1_seq": "SSDVGGYNF", "cdrl2_seq": "DVS", "cdrl3_seq": "SSYTSSSTFV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 116]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "7l5b", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2-15", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV2", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody 2-15 in complex with SARS-CoV-2 spike receptor-binding Domain"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 6914, 16, 22, 17, 2461, 12, 20733, 7390, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 1920, 8298, 1028, 3148, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1927, 1920, 14693, 1009, 17, 22, 2921, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 1930, 7131, 1927, 15667, 2321, 2353, 1930, 3292, 25780, 12526, 1990, 1920, 29177, 10429, 18, 3], "antigen": ["CPFGEVFNATRFASVYAWNRKRISNCVLYNSASFSTFKCYGVCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELL"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A human Fab, MJ20 (IGHV3/IGKV1-Kappa), targeting the C-terminal domain of the Nucleoprotein of Bundibugyo ebolavirus. The Nucleoprotein oligomerizes into a helical capsid to encapsidate the viral genome, protecting it from nucleases and the cellular innate immune response, and recruits host phosphatase to regulate viral transcription. The antibody is designed as a pan-specific diagnostic reagent capable of binding the C-terminal domains of nucleoproteins across all five known Ebola virus strains with high affinity.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVASSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFNISYSSIYSYSGYTARSYWYHVGSWHYTGMDY", "metadata": {"pdb_id": "5vkd", "light_chain_seq": "IQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRT", "cdrh1_seq": "GFNISYSS", "cdrh2_seq": "IYSYSGYT", "cdrh3_seq": "ARSYWYHVGSWHYTGMDY", "cdrl1_seq": "QSVSSA", "cdrl2_seq": "SAS", "cdrl3_seq": "QQSSSSLIT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "5w2b", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "MJ20", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Nucleoprotein, Bundibugyo ebolavirus", "target_domain": null, "functional_role": "other", "evidence_quote": "pan-specific Fab with the ability to bind selectively to the C-terminal domains of the nucleoproteins from all five known strains of the Ebola virus"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 15697, 3520, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 45, 17, 4262, 3418, 1927, 1920, 2797, 6657, 1927, 10051, 2023, 2215, 25749, 24497, 11074, 18, 1920, 2797, 6657, 13034, 4517, 2460, 43, 11514, 14681, 1942, 10771, 21550, 1920, 4324, 3843, 16, 15145, 2176, 2037, 29305, 1930, 1920, 3689, 8539, 3743, 2644, 16, 1930, 18855, 4423, 8167, 1942, 5741, 4324, 3213, 18, 1920, 3533, 1977, 4609, 1966, 43, 3797, 17, 2487, 4785, 7916, 7131, 1927, 2743, 1920, 45, 17, 4262, 4682, 1927, 2797, 14070, 3436, 2136, 3628, 3171, 24497, 3413, 4046, 1956, 2149, 5173, 18, 3], "antigen": ["AMANAQSEQSIAEMYQHILKTQGPFDAILYYHMMKEEPIIFSTSDGKEYTYPDSLEDEYPPWLSEKEAMNEDNRFITMDGQQFYWPVMNHRNKFMAILQHHR"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human single-chain Fv (scFv), R11 (IGHV1/IGKV1-Kappa), targeting the Kringle domain of the Inactive tyrosine-protein kinase transmembrane receptor ROR1, a tumor-associated antigen expressed in hematologic and solid malignancies. ROR1 is a receptor for WNT5A that activates downstream NFkB signaling and may enhance oncogenic CREB signaling via IGFBP5 and ERBB2 interactions. The antibody is designed as a T cell-engaging bispecific antibody (ROR1 \u00d7 CD3 scFv-Fc format) targeting a membrane-proximal epitope to recruit and activate cytolytic T cells against ROR1-expressing tumor cells. Can you generate its HCDRs?", "target_protein": "VKESEGDLVTPAGNLTLTCTASISWVRQAPGKGLEWIGFWYASWVKGRFTISRTSTTVDLKMTSLTTDDTATYFCWGPGTLVTISGSDINDYPINSGGSTARGYSTYYGDFNI", "metadata": {"pdb_id": "6ba5", "light_chain_seq": "ELVMTQTPSSTSGAVGGTVTINCQASQSIDSNLAWFQQKPGQPPTLLIYRASNLASGVPSRFSGSRSGTEYTLTISGVQREDAATYYCLGGVGNVSYRTSFGGGTEVVVK", "cdrh1_seq": "GSDINDYP", "cdrh2_seq": "INSGGST", "cdrh3_seq": "ARGYSTYYGDFNI", "cdrl1_seq": "QSIDSN", "cdrl2_seq": "RAS", "cdrl3_seq": "LGGVGNVSYRTS", "cdrh1_pos": "[22, 29]", "cdrh2_pos": "[47, 53]", "cdrh3_pos": "[90, 102]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 99]", "cdrh3_split": "val", "cdrh3_cluster": "6ban", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "R11", "antibody_format": "scFv", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Inactive tyrosine-protein kinase transmembrane receptor ROR1, Homo sapiens", "target_domain": "Kringe", "functional_role": "other", "evidence_quote": "T cell-engaging bispecific antibody targeting ROR1 with potent and selective antitumor activity"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 2957, 17, 4659, 11417, 12, 19863, 13, 16, 12041, 1009, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 6203, 1941, 1952, 3418, 1927, 1920, 9078, 6941, 17, 2213, 4016, 9117, 3148, 17399, 1009, 16, 43, 2798, 17, 2458, 4730, 3198, 1922, 18251, 1930, 5358, 10672, 18, 17399, 1009, 1977, 43, 3148, 1958, 26630, 1988, 9094, 5863, 4651, 11228, 3197, 1930, 2278, 4826, 11446, 13268, 3197, 3454, 16568, 1015, 1930, 17291, 3719, 18, 1920, 3533, 1977, 4609, 1966, 43, 62, 2024, 17, 15888, 7266, 10231, 3533, 12, 17399, 1009, 105, 9016, 19863, 17, 6437, 10387, 13, 5133, 43, 3260, 17, 6863, 10095, 1942, 5608, 1930, 6980, 29198, 62, 2094, 3316, 17399, 1009, 17, 4590, 2798, 2094, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["KCYNSTGVDYRGTVSVTKSGRQCQPWNSQYPHTHTFTALRFPELNGGHSYCRNPGNQKEAPWCFTLDENFKSDLCDIPAC"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A human Fab, DH511.2_K3 (IGHV3/IGKV1-Kappa), a chimeric antibody composed of the memory B cell DH511.2 heavy chain paired with the plasma-derived DH511.8P light chain, targeting the gp41 MPER peptide of Human immunodeficiency virus 1. The gp41 MPER is part of the envelope glycoprotein that mediates fusion of viral and host cell membranes during entry. The antibody is designed as a broadly neutralizing antibody targeting the distal MPER, binding within the MPER domain, and recognizing a transiently exposed intermediate conformation of gp41 that is exposed during the virion-host cell fusion process.", "target_protein": "QVQLVQSGGGLVKPGGSLTLSCSASMGWVRQAPGKGLEWVGREYGAAVKDRFTISRDDSRNMLYLHMRTLKTEDSGTYYCWGRGTTVIVSSAGFFFDNSWIRRLKDGATGTMDEGTPVTRFLEWGYFYYYMAV", "metadata": {"pdb_id": "5u3o", "light_chain_seq": "DIQMTQSPSFLYGSVGDRVTITCRASQNIKDYLNWYQQRPGRAPRLLIYAASNLQSGVPSRFSGSGYGTDFTLIISSLQPEDFATYFCQESYSSTPTHIFGLGTKLEKKRT", "cdrh1_seq": "GFFFDNSW", "cdrh2_seq": "IRRLKDGATG", "cdrh3_seq": "TMDEGTPVTRFLEWGYFYYYMAV", "cdrl1_seq": "QNIKDY", "cdrl2_seq": "AAS", "cdrl3_seq": "QESYSSTPTHI", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 120]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "5u3m", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DH511.2_K3", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "gp41 MPER peptide, Human immunodeficiency virus 1", "target_domain": "MPER; binding to GalCer", "functional_role": "neutralizing", "evidence_quote": "neutralized 206 of 208 (99%) global isolates with greater breadth and potency compared with 10E8"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6781, 7912, 1009, 18, 22, 41, 22949, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 43, 12727, 3533, 7179, 1927, 1920, 4525, 44, 2024, 6781, 7912, 1009, 18, 22, 7881, 4659, 7304, 1956, 1920, 3582, 17, 3595, 6781, 7912, 1009, 18, 28, 1034, 3696, 4659, 16, 5133, 1920, 25618, 5438, 1915, 4207, 1927, 2616, 13141, 3413, 21, 18, 1920, 25618, 5438, 1915, 1977, 3131, 1927, 1920, 11262, 11424, 1988, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 6583, 5438, 1915, 16, 2743, 2651, 1920, 5438, 1915, 3418, 16, 1930, 15667, 43, 12145, 4616, 6129, 7748, 1927, 25618, 1988, 1977, 4616, 2409, 1920, 19230, 17, 4423, 2024, 5289, 2585, 18, 3], "antigen": ["KWNWFDITNWLWYIRKK"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A murine Fab (IGHV1/IGKV5-Kappa) targeting the Gametocyte surface protein P230 of Plasmodium falciparum. The Gametocyte surface protein P230 is required for male and female gamete fusion, male gamete exflagellation, and interaction with host erythrocytes. The antibody is designed as a transmission-blocking antibody that sterically interferes with protein\u2013protein interactions required for parasite transmission to the mosquito vector.", "target_protein": "QVQLQQPGAELVKPGASVQLSCKASMHWVKQRPGQGLEWIGMNFNEKLKSKVTLTVDKSSTTAYMQLSSLTSEDAAVYYCWGTGTTVTVSSAGYTFTSYWIHPTNDKTARSLSAYWYFDV", "metadata": {"pdb_id": "6ohg", "light_chain_seq": "DILLTQSPAILSVSPGERVSFSCRASQSIGTSIHWYQQKTQGSPRLLIKYSSESISGIPSRFSGSGAGTDFTLSINSVESEDIAVFYCQQSYTWPIFTFGSGTKLEIKRA", "cdrh1_seq": "GYTFTSYW", "cdrh2_seq": "IHPTNDKT", "cdrh3_seq": "ARSLSAYWYFDV", "cdrl1_seq": "QSIGTS", "cdrl2_seq": "YSS", "cdrl3_seq": "QQSYTWPIFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "6ohg", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV5", "is_engineered": false, "target_antigen": "Gametocyte surface protein P230, Plasmodium falciparum", "target_domain": null, "functional_role": "other", "evidence_quote": "transmission blocking antibody; reduces transmission in SMFA assay"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1015, 17, 12093, 13, 5133, 1920, 21009, 4463, 3154, 2213, 7535, 4294, 1927, 15663, 13098, 18, 1920, 21009, 4463, 3154, 2213, 7535, 4294, 1977, 3414, 1958, 4005, 1930, 4232, 21009, 1021, 5289, 16, 4005, 21009, 1021, 1975, 20631, 30439, 16, 1930, 2835, 1956, 4423, 14161, 18, 1920, 3533, 1977, 4609, 1966, 43, 5303, 17, 7472, 3533, 1988, 17638, 2169, 20766, 1956, 2213, 229, 2213, 3719, 3414, 1958, 8652, 5303, 1942, 1920, 9719, 4580, 18, 3], "antigen": ["DLSYETTESGDTAVSEDSYDKYASQNTNKEYVCDFTDQLKPTESGPKVKKCEVKVNEPLIKVKIICPLKGSVEKLYDNIEYVPKKSPYVVLTKEETKLKEKLLSKLIYGLLISPTVNEKENNFKEGVIEFTLPPVVHKATVFYFICDNSKTEDDNKKGNRGIVEVYVEPY"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab (IGHV3/IGLV3-Lambda) targeting the engineered Non-structural protein 1 of Zika virus. Non-structural protein 1 functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter, and also inhibits the integrated stress response in infected cells. This antibody forms a complex with Non-structural protein 1. Please output the HCDRs.", "target_protein": "VELIESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVAFYYADSVKGRFTISRDNSKNTLSLQMNSLRAEDTALYYCWGQGTLVTVSSGFTFSNYAISYDGSNKARVFNGYEGDY", "metadata": {"pdb_id": "8jqn", "light_chain_seq": "LTQPPSVSVSPGQTARITCSGDALPKKYAYWYQQKSGQAPVLVIYEDSKRPSGIPERFSGSSSGTMATLTISGAQVEDEADYYCYSTDSSGNLYVFGTGTKVTVL", "cdrh1_seq": "GFTFSNYA", "cdrh2_seq": "ISYDGSNK", "cdrh3_seq": "ARVFNGYEGDY", "cdrl1_seq": "ALPKKY", "cdrl2_seq": "EDS", "cdrl3_seq": "YSTDSSGNLYV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 105]", "cdrl1_pos": "[22, 27]", "cdrl2_pos": "[45, 47]", "cdrl3_pos": "[84, 94]", "cdrh3_split": "val", "cdrh3_cluster": "8jqn", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV3", "is_engineered": true, "target_antigen": "Non-structural protein 1, Zika virus", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 28961, 1020, 1010, 17, 18279, 13, 5133, 1920, 11091, 2447, 17, 4346, 2213, 21, 1927, 28593, 3413, 18, 2447, 17, 4346, 2213, 21, 4088, 1966, 43, 2733, 4207, 1958, 4246, 14919, 1930, 1977, 3414, 1958, 1920, 10001, 18394, 2455, 1927, 1920, 6296, 16, 1930, 2222, 7042, 1920, 6714, 3071, 2644, 1922, 4014, 2094, 18, 2052, 3533, 4952, 43, 2796, 1956, 2447, 17, 4346, 2213, 21, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["HHHHGCSVDFSKKETRCGTGVFVYNDVEAWRDRYKYHPDSPRRLAAAVKQAWEDGICGISSVSRMENIMWRSVEGELNAILEENGVQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGKSYFVRAAKTNNSFVVDGDTLKECPLKHRAWNSFLVEDHGFGVFHTSVWLKVREDYSLECDPAVIGTAVKGKEAVHSDLGYWIESEKNDTWRLKRAHLIEMKTCEWPKSHTLWTDGIEESDLIIPKSLAGPLSHHNTREGYRTQMKGPWHSEELEIRFEECPGTKVHVEETCGTRGPSLRSTTASGRVIEEWCCRECTMPPLSFRAKDGCWYGMEIRPRKEPESNLVRSMVTA"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A human Fab, B11 (IGHV4/IGKV3-Kappa), targeting the Outer surface protein C of Borreliella burgdorferi. Outer surface protein C is a major immunodominant protein required for initial stages of mammalian infection, interacts with tick salivary proteins to evade antibody-mediated killing, inhibits macrophage-mediated phagocytosis, and binds human plasminogen and complement C4-B. The antibody is designed as a bactericidal antibody targeting the homodimeric OspC, engaging the membrane-proximal regions and spanning the dimer interface.", "target_protein": "QLQLQESGPGLVKPSQTLSLTCTLSWGWIRQPPGSGLEWIGSYYKSSLKGRVTISLDTSRTQFSLRLTSVTAADTAVYYCWGQGTTVIVSSAGGSISSTSYMYHSGNTARLGDVFNSAMDV", "metadata": {"pdb_id": "9bif", "light_chain_seq": "EIVMTQSPVTLSVSPGERATLSCRASQSVGNNLAWYQHKPGQAPRLLIYDASTRATGIPGRFSGSGSGTEFTLTISSLQSEDFAVYYCQEYNNWPRYTFGQGAKLEIRRT", "cdrh1_seq": "GGSISSTSY", "cdrh2_seq": "MYHSGNT", "cdrh3_seq": "ARLGDVFNSAMDV", "cdrl1_seq": "QSVGNN", "cdrl2_seq": "DAS", "cdrl3_seq": "QEYNNWPRYT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "9bif", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "B11", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Outer surface protein C, Borreliella burgdorferi", "target_domain": null, "functional_role": "other", "evidence_quote": "patient-derived bactericidal monoclonal IgG against outer surface protein C"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 10360, 1009, 12, 20733, 1020, 1006, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 7642, 3154, 2213, 45, 1927, 27037, 19918, 24902, 18, 7642, 3154, 2213, 45, 1977, 43, 3044, 6595, 5081, 3560, 2213, 3414, 1958, 3754, 5143, 1927, 6492, 2909, 16, 9034, 1956, 12085, 11866, 2697, 1942, 28917, 3533, 17, 3434, 11879, 16, 7042, 8088, 17, 3434, 13715, 16, 1930, 6876, 2616, 17485, 1930, 5508, 10872, 17, 44, 18, 1920, 3533, 1977, 4609, 1966, 43, 20659, 3533, 5133, 1920, 21189, 1935, 3125, 7693, 16, 15888, 1920, 3260, 17, 6863, 3451, 1930, 13346, 1920, 7632, 6854, 18, 3], "antigen": ["ISKKITDSNAVLLAVKEVEALLSSIDEIAAKAIGKKIHQNNGLDTENNHNGSLLAGAYAISTLIKQKLDGLKNEGLKEKIDAAKKCSETFTNKLKEKHTDLGKEGVTDADAKEAILKTNGTKTKGAEELGKLFESVEVLSKAAKEMLANSVKELTSP"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A murine Fab (IGHV1/IGKV6-Kappa) targeting an engineered Proprotein convertase subtilisin/kexin type 9 (PCSK9) of Homo sapiens. PCSK9 is a crucial player in the regulation of plasma cholesterol homeostasis, binding to low-density lipoprotein receptor family members and promoting their degradation in intracellular acidic compartments. The antibody is designed as a PCSK9 antagonist that inhibits PCSK9 binding to LDLR and preserves cellular LDLR levels. Please generate its HCDRs.", "target_protein": "QVQLKQSGAELVRPGASVKLSCKASINWLKKRPGQGLEWIARYYNENFKDKATLTAEKSSSNVYMQLSSLTSEDSAVYFCWGTGTTVTVSSAGYIFTDYYIYPGSGHTARENFYGSSYVDWYFDV", "metadata": {"pdb_id": "6u3i", "light_chain_seq": "DIVMTQSQKFMSTSGGDRVSITCKTSQNVGTAVAWFQQKPGQSPKLLIYSASNRYTGVSDRFTGSGSGTEFIFTISYAQSEDLADYFCHQYSSYPLTFGAGTKLELKRA", "cdrh1_seq": "GYIFTDYY", "cdrh2_seq": "IYPGSGHT", "cdrh3_seq": "ARENFYGSSYVDWYFDV", "cdrl1_seq": "QNVGTA", "cdrl2_seq": "SAS", "cdrl3_seq": "HQYSSYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7bh8", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Proprotein convertase subtilisin/kexin type 9, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "inhibited PCSK9 binding to LDLR and preserved cellular LDLR"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 5133, 1925, 11091, 12031, 7229, 1921, 14450, 2051, 14745, 1921, 19, 3364, 10960, 2601, 29, 12, 26601, 13, 1927, 16350, 27974, 18, 26601, 1977, 43, 6608, 18316, 1922, 1920, 3640, 1927, 3582, 5463, 7622, 16, 2743, 1942, 2330, 17, 3824, 9694, 3148, 3416, 4678, 1930, 7356, 2310, 4877, 1922, 4776, 9931, 10436, 18, 1920, 3533, 1977, 4609, 1966, 43, 26601, 8151, 1988, 7042, 26601, 2743, 1942, 20944, 1930, 29256, 3689, 20944, 2428, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRDAVTAVAICCRSR"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A human Fab, 16.ND.92 (IGHV3/IGKV1-Kappa), targeting the Hemagglutinin of Influenza A virus (A/Solomon Islands/3/2006(H1N1)). Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and is a class I viral fusion protein responsible for penetration into the cell cytoplasm by mediating membrane fusion. The antibody is designed as a neutralizing antibody targeting the HA stem, with in vivo protection activity against both H1N1 and H5N1 strains. Generate the corresponding HCDRs.", "target_protein": "VQLVESGGGLVQPGGSLRLSCEASMHWVRQDPGKGLVWVAVDYADFVKGRFTISRDNAKNTVYLQMNSLRAEDTAVYYCWGQGTMVTVSSGFTLSSYWINSDGSSTARAPQGTVFGVVIIGADGFDI", "metadata": {"pdb_id": "9cu7", "light_chain_seq": "IQMTHIPVSLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASTLESGVPSRFSGSGSGTDFTLTINSLQPDDFATYYCQHYNTYSRAWTFGQGTKVEV", "cdrh1_seq": "GFTLSSYW", "cdrh2_seq": "INSDGSST", "cdrh3_seq": "ARAPQGTVFGVVIIGADGFDI", "cdrl1_seq": "QSISSW", "cdrl2_seq": "KAS", "cdrl3_seq": "QHYNTYSRAWT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 115]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 97]", "cdrh3_split": "val", "cdrh3_cluster": "9cu7", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "16.ND.92", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus (A/Solomon Islands/3/2006(H1N1))", "target_domain": "HA stem", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibodies with in vivo protection activity against H1N1 and H5N1"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 2641, 18, 8026, 18, 6224, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 12, 43, 19, 2638, 20050, 13408, 19, 23, 19, 3956, 12, 15355, 13, 13, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 1977, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 12006, 2460, 1920, 2024, 5239, 2007, 10239, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 2118, 4402, 16, 1956, 1922, 3597, 6202, 2455, 3316, 2321, 15355, 1930, 20128, 4046, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["LFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMNTQFTAVGKEFNKLERRMENLNKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKYSEESKLNR", "DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGIAPLQLGNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEVLVLWGVHHPPNIGDQRALYHKENAYVSVVSSHYSRKFTPEIAKRPKVRDQEGRINYYWTLLEPGDTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSAKLRMVTGLRNIP"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A human Fab, C2H7 (IGHV1/IGKV4-Kappa), targeting the B-lymphocyte antigen CD20 of Homo sapiens. CD20 is a B-lymphocyte-specific membrane protein that regulates cellular calcium influx necessary for B-lymphocyte development, differentiation, and activation, functioning as a store-operated calcium channel component. The antibody is designed to mediate complement-dependent cytotoxicity and antibody-dependent cellular cytotoxicity against CD20-positive B-cell lymphomas.", "target_protein": "QAYLQQSGAELVRPGASVKMSCKASMHWVKQTPRQGLEWIGASYNQKFKGKATLTVDKSSSTAYMQLSSLTSEDSAVYFCWGTGTTVTVSAAGYTFTSYNIYPGNGDTARVVYYSNSYWYFDV", "metadata": {"pdb_id": "3bky", "light_chain_seq": "QIVLSQSPAILSASPGEKVTMTCRASSSVSYMHWYQQKPGSSPKPWIYAPSNLASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQWSFNPPTFGAGTKLELKRT", "cdrh1_seq": "GYTFTSYN", "cdrh2_seq": "IYPGNGDT", "cdrh3_seq": "ARVVYYSNSYWYFDV", "cdrl1_seq": "SSVSY", "cdrl2_seq": "APS", "cdrl3_seq": "QQWSFNPPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "3bky", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "C2H7", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "B-lymphocyte antigen CD20, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "mediate complement dependent cytotoxicity and antibody-dependent cellular cytotoxicity effects on CD20 positive human Burkitt lymphoma cells"}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 8453, 1023, 1027, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 16, 5133, 1920, 44, 17, 10009, 4730, 16494, 1927, 16350, 27974, 18, 16494, 1977, 43, 44, 17, 10009, 17, 2487, 3260, 2213, 1988, 7014, 3689, 5016, 12403, 4680, 1958, 44, 17, 10009, 2740, 16, 4155, 16, 1930, 2936, 16, 7295, 1966, 43, 14582, 17, 10497, 5016, 4999, 4594, 18, 1920, 3533, 1977, 4609, 1942, 8265, 5508, 17, 3100, 8470, 1930, 3533, 17, 3100, 3689, 8470, 3316, 16494, 17, 2843, 44, 17, 2024, 16827, 18, 3], "antigen": ["CEPANPSEKNSPSTQYC"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the engineered Spike protein S1 of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that binds the BQ.1.1 variant RBD through conformational selection, binding within the Receptor-binding domain (RBD).", "target_protein": "VQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "8fxc", "light_chain_seq": "IVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKV", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 114]", "cdrl1_pos": "[25, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike protein S1, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "sotrovimab binds avidly to all Omicron variants, promotes Fc-dependent effector functions and protects mice"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 2213, 4062, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 6876, 1920, 26393, 18, 21, 18, 21, 6031, 25780, 2596, 8523, 4367, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 3], "antigen": ["NLCPFDEVFNATTFASVYAWNRKRISNCVADYSVLYNFAFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSTVGGNYNYRYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFETVCGP"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A human Fab (IGHV1/IGKV3-Kappa) targeting the engineered SARS-CoV-2 XBB.1.5 RBD, the receptor-binding domain of the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with the host ACE2 receptor to initiate infection. The antibody is designed as a pan-sarbecovirus neutralizing antibody with high tolerance for epitope diversification, binding within the BetaCoV S1-CTD and targeting the receptor-binding motif with extensive backbone contacts that remain invariant across RBD mutations.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "9au1", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "BetaCoV S1-CTD", "functional_role": "neutralizing", "evidence_quote": "neutralizes all SARS-CoV-2 variants that have arisen thus far"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 11091, 20466, 17, 6083, 17, 22, 20584, 1014, 18, 21, 18, 25, 25780, 16, 1920, 3148, 17, 2743, 3418, 1927, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 1920, 4423, 8298, 1028, 3148, 1942, 11051, 2909, 18, 1920, 3533, 1977, 4609, 1966, 43, 3797, 17, 9851, 12409, 7414, 12130, 3533, 1956, 2149, 6555, 1958, 10095, 20046, 16, 2743, 2651, 1920, 4666, 4879, 1020, 4062, 17, 15898, 1930, 5133, 1920, 3148, 17, 2743, 5219, 1956, 6475, 10787, 9070, 1988, 5555, 17004, 3436, 25780, 3527, 18, 3], "antigen": ["TNLCPFHEVFNATTFASVYAWNRKRISNCVADYSVIYNFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPK"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A murine Fab, D12 (IGHV5/IGKV10-Kappa), targeting the Spike glycoprotein of Human coronavirus EMC (MERS-CoV, isolate United Kingdom/H123990006/2012). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host DPP4 receptor to initiate infection and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody elicited by DNA prime-protein boost vaccination, binding within the BetaCoV S1-CTD and targeting the receptor-binding motif to prevent DPP4 engagement. Please generate the HCDRs for this antibody.", "target_protein": "EVKLVESGGGLVKPGGSLKLSCAASMSWVRQTPEKRLEWVATYYPDSVKGRFTISRDNAENTLYLQMSSLRSEDTAMYYCWGQGTSVTVSSAGFTFSSYAISSGGTYTVRDGNSMDY", "metadata": {"pdb_id": "4zpv", "light_chain_seq": "DIQMTQTTSSLSASLGDRVTIICRASQDINNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGSDYSLTISNLEQEDIATYFCQQANTLPPTFGAGTKLELRRA", "cdrh1_seq": "GFTFSSYA", "cdrh2_seq": "ISSGGTYT", "cdrh3_seq": "VRDGNSMDY", "cdrl1_seq": "QDINNY", "cdrl2_seq": "YTS", "cdrl3_seq": "QQANTLPPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 104]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "4zpt", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "D12", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV10", "is_engineered": false, "target_antigen": "Spike glycoprotein, Human coronavirus EMC (isolate United Kingdom/H123990006/2012)", "target_domain": "BetaCoV S1-CTD", "functional_role": "neutralizing", "evidence_quote": "vaccine-elicited murine neutralizing antibody D12"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 8524, 1028, 12, 20733, 1020, 1015, 19, 7021, 1040, 7390, 1008, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 2616, 5548, 10703, 2391, 1030, 12, 20197, 17, 6083, 16, 9158, 6128, 13543, 19, 21907, 6021, 5124, 23959, 19, 3775, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 16423, 1006, 3148, 1942, 11051, 2909, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 9856, 2007, 2678, 13476, 17, 2213, 17067, 7507, 16, 2743, 2651, 1920, 4666, 4879, 1020, 4062, 17, 15898, 1930, 5133, 1920, 3148, 17, 2743, 5219, 1942, 4625, 16423, 1006, 9577, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKL"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A human Fab, necitumumab (IGHV4/IGKV3-Kappa), targeting an engineered variant of the Epidermal growth factor receptor (EGFR domain III with S468R substitution). EGFR is a receptor tyrosine kinase that binds ligands of the EGF family and activates multiple downstream signaling cascades to convert extracellular cues into appropriate cellular responses. The antibody is designed to retain binding and inhibitory activity against cetuximab-resistant EGFR variants, particularly the S468R substitution, through accommodation of the arginine residue within a large paratope cavity that permits binding while maintaining blockade of ligand-induced EGFR activation and induction of receptor internalization and degradation.", "target_protein": "QVQLQESGPGLVKPSQTLSLTCTVSWSWIRQPPGKGLEWIGYDYNPSLKSRVTMSVDTSKNQFSLKVNSVTAADTAVYYCWGQGTLVTVSSAGGSISSGDYYIYYSGSTARVSIFGVGTFDY", "metadata": {"pdb_id": "6b3s", "light_chain_seq": "EIVMTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCHQYGSTPLTFGGGTKAEIKRT", "cdrh1_seq": "GGSISSGDYY", "cdrh2_seq": "IYYSGST", "cdrh3_seq": "ARVSIFGVGTFDY", "cdrl1_seq": "QSVSSY", "cdrl2_seq": "DAS", "cdrl3_seq": "HQYGSTPLT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3b2u", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "necitumumab", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Epidermal growth factor receptor, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "necitumumab binds to EGFR-S468R and retains inhibitory activities including blockade of ligand-induced EGFR activation and induction of receptor internalization and degradation"}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 3296, 13378, 6683, 12, 20733, 1020, 1006, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1925, 11091, 6031, 1927, 1920, 9844, 2905, 2991, 3148, 12, 5775, 3418, 4337, 1956, 6934, 6735, 1005, 6636, 13, 18, 5775, 1977, 43, 3148, 6941, 4016, 1988, 6876, 6908, 1927, 1920, 4451, 3416, 1930, 9094, 3137, 5863, 3197, 15967, 1942, 14450, 5329, 8972, 2460, 4703, 3689, 3387, 18, 1920, 3533, 1977, 4609, 1942, 13562, 2743, 1930, 5431, 2455, 3316, 19418, 17, 4910, 5775, 4936, 16, 4443, 1920, 6934, 6735, 1005, 6636, 16, 2596, 24723, 1927, 1920, 9732, 6181, 2651, 43, 3103, 24940, 4907, 8568, 1988, 16299, 2743, 2679, 8231, 9847, 1927, 5207, 17, 2719, 5775, 2936, 1930, 4408, 1927, 3148, 12071, 1930, 4877, 18, 3], "antigen": ["EKKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIIRNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSC"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A murine Fab, Ky15.10 (IGHV3/IGKV1-Kappa), targeting the Circumsporozoite protein of Plasmodium falciparum (isolate NF54). The Circumsporozoite protein is essential for sporozoite development, migration through the vector and host, and infection of host hepatocytes through binding to heparan sulfate proteoglycans on hepatocyte surfaces. The antibody is designed as a neutralizing antibody that inhibits sporozoite traversal and parasite liver invasion, adopting the 1210-like binding mode that confers cross-reactivity to junctional PfCSP repeat motifs.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQVPGKGLEWVAIYYADSVKGRFSVSRDNSENTLYLQMSNLRAEDTAVYYCWGQGTTVTVSSAGFTFSNSGIWYDGSNKVRAYFDSENLYDYYGMDV", "metadata": {"pdb_id": "8fb6", "light_chain_seq": "DIQMTQSPSTLSASVGDRVTITCRASQSISRWLAWFQKKPGKAPKLLIYTASNLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYYNYWTFGQGTKVEVKRT", "cdrh1_seq": "GFTFSNSG", "cdrh2_seq": "IWYDGSNK", "cdrh3_seq": "VRAYFDSENLYDYYGMDV", "cdrl1_seq": "QSISRW", "cdrl2_seq": "TAS", "cdrl3_seq": "QQYYNYWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "8fa6", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Ky15.10", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Circumsporozoite protein, Plasmodium falciparum (isolate NF54)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "effectively inhibited Pf sporozoite traversal in vitro and reduced parasite liver load in vivo"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 13995, 3962, 18, 2119, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 28868, 2074, 26553, 2213, 1927, 15663, 13098, 12, 9158, 4651, 5651, 13, 18, 1920, 28868, 2074, 26553, 2213, 1977, 4415, 1958, 9130, 26553, 2740, 16, 5049, 2596, 1920, 4580, 1930, 4423, 16, 1930, 2909, 1927, 4423, 9919, 2596, 2743, 1942, 22024, 8767, 25185, 1990, 14675, 7553, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7042, 9130, 26553, 27480, 1923, 1930, 8652, 3568, 6254, 16, 20478, 1920, 11844, 1008, 17, 3189, 2743, 5754, 1988, 16556, 3567, 17, 8229, 1942, 21226, 14425, 3508, 6865, 8277, 18, 3], "antigen": ["GNPDPNANPN"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A murine Fab (IGHV1/IGKV16-Kappa) targeting the cytochrome c-dependent nitric oxide reductase (cNOR) complex, comprising Nitric oxide reductase subunits B and C from Pseudomonas aeruginosa. The cNOR complex catalyzes the reductive coupling of two nitric oxide molecules at a heme/non-heme Fe center to generate nitrous oxide, and functions as a component of the anaerobic respiratory chain in denitrification. This antibody is intended as a structural tool to facilitate crystallographic determination of the enzyme in reduced and ligand-bound states. Please generate the HCDRs for this antibody.", "target_protein": "EVQLQQSGTVLARPGASVKMSCKASMHWVKQRPGQGLEWIGASYNQKFKGKAKLTAVTSASTAYMELSSLTNEDSAVYYCWGQGTTVTVSSAGYSFTSYWVYPGNSDTSRSSLDGYYVKNWCFDV", "metadata": {"pdb_id": "3wfd", "light_chain_seq": "DIQMTQSPPYLAASPGETITINCRASKSIRKYLAWYQEKPGKTNKLLIYSGSTLQFGIPSRFSGSGSGTEFTLTISSLEPEDFAMYYCQQHNEYPLTFGAGTKLELKRA", "cdrh1_seq": "GYSFTSYW", "cdrh2_seq": "VYPGNSDT", "cdrh3_seq": "SRSSLDGYYVKNWCFDV", "cdrl1_seq": "KSIRKY", "cdrl2_seq": "SGS", "cdrl3_seq": "QQHNEYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3o0r", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV16", "is_engineered": false, "target_antigen": "Nitric oxide reductase subunits B and C, Pseudomonas aeruginosa", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "antibody fragment used to determine structures of reduced and ligand-bound cNOR"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 1016, 17, 12093, 13, 5133, 1920, 9387, 45, 17, 3100, 10233, 7491, 11386, 12, 5940, 1924, 13, 2796, 16, 10351, 10233, 7491, 11386, 6991, 44, 1930, 45, 2037, 13461, 10830, 18, 1920, 5940, 1924, 2796, 17097, 1920, 23335, 7590, 1927, 2288, 10233, 7491, 4206, 2019, 43, 10954, 19, 2447, 17, 10954, 2650, 4102, 1942, 5655, 8686, 1957, 7491, 16, 1930, 4088, 1966, 43, 4594, 1927, 1920, 12554, 5481, 4659, 1922, 26319, 3123, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 6628, 17832, 7063, 1927, 1920, 4113, 1922, 3028, 1930, 5207, 17, 4124, 4376, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["FASQAVAKPYFVFALILFVGQILFGLIMGLQYVVGDFLFPAIPFNVARMVHTNLLIVWLLFGFMGAAYYLVPEESDCELYSPKLAWILFWVFAAAGVLTILGYLLVPYAGLARLTGNELWPTMGREFLEQPTISKAGIVIVALGFLFNVGMTVLRGRKTAISMVLMTGLIGLALLFLFSFYNPENLTRDKFYWWWVVHLWVEGVWELIMGAILAFVLVKITGVDREVIEKWLYVIIAMALISGIIGTGHHYFWIGVPGYWLWLGSVFSALEPLPFFAMVLFAFNTINRRRRDYPNRAVALWAMGTTVMAFLGAGVWGFMHTLAPVNYYTHGTQLTAAHGHMAFYGAYAMIVMTIISYAMPRLRGIGEAMDNRSQVLEMWGFWLMTVAMVFITLFLSAAGVLQVWLQRMPADGAAMTFMATQDQLAIFYWLREGAGVVFLIGLVAYLLSF", "FTKGMARNIYFGGSVFFILLFLALTYHTEKTLPERTNEAAMSAAVVRGKLVWEQNNCVGCHTLLGEGAYFAPELGNVVGRRGGEEGFNTFLQAWMKIQPLNVPGRRAMPQFHLSEGQVDDLAEFLKWSSKIDTNQWPPNKEG"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A human Fab, 0722 (IGHV1/IGKV1-Kappa), targeting the Spike glycoprotein of Middle East respiratory syndrome-related coronavirus. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host DPP4 receptor to initiate infection and mediates fusion of viral and cellular membranes through conformational transitions from pre-fusion to post-fusion states. This antibody forms a complex with the Spike glycoprotein ectodomain trimer.", "target_protein": "QVQLVQSGAEVKKPGSSVKVSCKASISWVRQAPGQGLEWMGGNYAQQFQGRVTITADESTTTAYMELSRLTSEDTAVYYCWGQGTLVTVSSAGGTFSIYAIIPIFGTAARQMTAYDYWNPSFDY", "metadata": {"pdb_id": "7v5k", "light_chain_seq": "DIVMTQTPSSLSASVGDRVTITCRASEDITSYLNWYQLKPGKAPMFLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPTFGGGTKVEIKRT", "cdrh1_seq": "GGTFSIYA", "cdrh2_seq": "IIPIFGTA", "cdrh3_seq": "ARQMTAYDYWNPSFDY", "cdrl1_seq": "EDITSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSYSTPPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7v5j", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "0722", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Spike glycoprotein, Middle East respiratory syndrome-related coronavirus", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 2616, 6914, 16, 6627, 4460, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 5576, 10319, 5481, 4741, 17, 2712, 5548, 10703, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 16423, 1006, 3148, 1942, 11051, 2909, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 10673, 2037, 2097, 17, 5289, 1942, 2753, 17, 5289, 4376, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 11424, 27385, 20085, 18, 3], "antigen": ["YVDVGPDSVKSACIEVDIQQTFFDKTWPRPIDVSKADGIIYPQGRTYSNITITYQGLFPYQGDHGDMYVYSAGHATGTTPQKLFVANYSQDVKQFANGFVVRIGAAANSTGTVIISPSTSATIRKIYPAFMLGSSVGNFSDGKMGRFFNHTLVLLPDGCGTLLRAFYCILEPRSGNHCPAGNSYTSFATYHTPATDCSDGNYNRNASLNSFKEYFNLRNCTFMYTYNITEDEILEWFGITQTAQGVHLFSSRYVDLYGGNMFQFATLPVYDTIKYYSIIPHSIRSIQSDRKAWAAFYVYKLQPLTFLLDFSVDGYIRRAIDCGFNDLSQLHCSYESFDVESGVYSVSSFEAKPSGSVVEQVECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKLKIASQLGNCVEYSLYGVSGRGVFQNCTAVGVRQQRFVYDAYQNLVGYYSDDGNYYCLRACVSVPVSVIYDKETKTHATLFGSVACEHISSTMSQYSRSTRSMLKPVGCVLGLVNSSLFVEDCKLPLGQSLCALPDTPSTMRLASIAFNHPIQVDQLNSSYFKLSIPTNFSFGVTQEYIQTTIQKVTVDCKQYVCNGFQKCEQLLREYGQFCSKINQALHGANLRQDDSVRNLFASVKSSQSSPIIPGFGGDFNLTLLEPVARSAIEDLLFDKVTIADPGYMQGYDDCMQQICAQYVAGYKVLPPLMDVNMEAAYTSSLLGSIAGVGWTAGLSSFAAIPFAQSIFYRLNGVGITQQVLSENQKLIANKFNQALGAMQTGFTTTNEAFQKVQDAVNNNAQALSKLASELSNTFGAISASIGDIIQRLDVLEQDAQIDRLINGRLTTLNAFVAQQLVRSESAALSAQLAKDKVNECVKAQSKRSGFCGQGTHIVSFVVNAPNGLYFMHVGYYPSNHIEVVSAYGLCDAANPTNCIAPVNGYFIKTNNTRIVDEWSYTGSSFYAPEPITSLNTKYVA"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A human Fab, 447-52D (IGHV3/IGLV1-Lambda), targeting the Envelope glycoprotein of Human immunodeficiency virus 1. The antibody is designed as a neutralizing antibody with broad activity against primary viral isolates, binding within the Human immunodeficiency virus 1 envelope glycoprotein Gp120, specifically targeting the third variable loop (V3).", "target_protein": "EVQLVESGGGLVKPGGSLRLTCVASLNWVRQAPGKGLEWVGRDYAASVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYSCWGKGTTVTVSSAGFTFSDVWIKSRTDGGTTTTDGFIMIRGVSEDYYYYYMDV", "metadata": {"pdb_id": "3c2a", "light_chain_seq": "QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVLWYQQFPGTAPKLLIYGNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYFCATWDSGLSADWVFGGGTKLTVLSQ", "cdrh1_seq": "GFTFSDVW", "cdrh2_seq": "IKSRTDGGTT", "cdrh3_seq": "TTDGFIMIRGVSEDYYYYYMDV", "cdrl1_seq": "SSNIGNNY", "cdrl2_seq": "GNN", "cdrl3_seq": "ATWDSGLSADWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 119]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 100]", "cdrh3_split": "val", "cdrh3_cluster": "4m1d", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "447-52D", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein, Human immunodeficiency virus 1", "target_domain": "Human immunodeficiency virus 1 envelope glycoprotein Gp120", "functional_role": "neutralizing", "evidence_quote": "exhibits relatively broad neutralization of primary viral isolates"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 29146, 17, 4764, 1007, 12, 20733, 1020, 1010, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 11262, 11424, 1927, 2616, 13141, 3413, 21, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1956, 4949, 2455, 3316, 3065, 4324, 5645, 16, 2743, 2651, 1920, 2616, 13141, 3413, 21, 11262, 11424, 16102, 16, 4475, 5133, 1920, 4563, 4650, 5881, 12, 14307, 13, 18, 3], "antigen": ["KSIHLGPGRAFYA"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A human Fab, 5E3 (IGHV3/IGKV3-Kappa), targeting the Core protein (NS1) of Dengue virus 2. The Core protein functions as a component of the viral RNA replication complex that antagonizes the host immune response and functions as a signal peptide for NS4B required for interferon antagonism activity. The antibody is designed to dissociate loose tetrameric and hexameric NS1 oligomeric states into dimers, thereby reducing NS1-induced endothelial hyperpermeability. Generate the corresponding HCDRs.", "target_protein": "QVQLVESGGGLVKPGGSLRLSCAASMSWIRQAPGKGLEWVSYDYADSVKGRFTISRDNTKNSLYLQLNSLRDEDTAVYYCWGQGTLVTVSSGFTFSDYYISTGSSHTASGYRFSYVSY", "metadata": {"pdb_id": "7wur", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASTRATGIPDRFTGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPAWTFGQGTKVEI", "cdrh1_seq": "GFTFSDYY", "cdrh2_seq": "ISTGSSHT", "cdrh3_seq": "ASGYRFSYVSY", "cdrl1_seq": "QSVSSSY", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYGSSPAWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "7wur", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "5E3", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Core protein (NS1), Dengue virus 2", "target_domain": null, "functional_role": "other", "evidence_quote": "Fab 5E3 can readily dissociate the sNS1 loose tetrameric and hexameric structures"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 14538, 1010, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 4728, 2213, 12, 19082, 13, 1927, 13304, 3413, 22, 18, 1920, 4728, 2213, 4088, 1966, 43, 4594, 1927, 1920, 4324, 3146, 5158, 2796, 1988, 28104, 1036, 1920, 4423, 3743, 2644, 1930, 4088, 1966, 43, 2733, 4207, 1958, 4246, 14919, 3414, 1958, 10001, 18394, 2455, 18, 1920, 3533, 1977, 4609, 1942, 26549, 21425, 30442, 1930, 25602, 1935, 19082, 19206, 4376, 2460, 13351, 16, 6113, 5526, 19082, 17, 2719, 5003, 4194, 2116, 3870, 2550, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["DSGCVVSWKNKELKCGSGIFITDNVHTWTEQYKFQPESPSKLASAIQKAHEEGICGIRSVTRLENLMWKQITPELNHILTENEVKLTIMTGDIKGIMQAGKRSLRPQPTELKYSWKAWGKAKMLSTELHNHTFLIDGPETAECPNTNRAWNSLEVEDYGFGVFTTNIWLKLKERQDVFCDSKLMSAAIKDNRAVHADMGYWIESALNDTWKIEKASFIEVKSCHWPKSHTLWSNGVLESEMIIPKNFAGPVSQHNYRPGYHTQTAGPWHLGRLEMDFDFCEGTTVVVTEDCGNRGPSLRTTTASGKLITEWCCRSCTLPPLRYRGEDGCWYGMEIRPLKEK"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab, DENV-290 (IGHV3/IGKV2-Kappa), targeting the Envelope protein of Dengue virus type 3. The Envelope protein is a component of the viral RNA replication complex that functions in virion assembly and antagonizes the host immune response. The antibody is designed as a neutralizing antibody that primarily blocks virus attachment to cells, binding at the center of the E protein dimer across domain II of two opposite protomers, defining a new EDE-C epitope class.", "target_protein": "QVELVESGGDVVQPGKSLRLSCAASMHWLRQAPGKGLEWVAVYYADSVKGRFTISRDNSKNTLYLQMNSLTPEDTAVYYCWGQGTLVTVSSGFTFTNYAISSDVNDKAREQAVGTNPWAFDY", "metadata": {"pdb_id": "8jn4", "light_chain_seq": "HIVMTQSPLSLSVTPGQPASISCKSSQISSWGSDGKTYLYWYLQKPGQSPQLLIYEVSSRFSGVSDRFSGSGSGTDFTLKISRVQAEDVGLYYCMQGLHLPLTFGQGTRLEIK", "cdrh1_seq": "GFTFTNYA", "cdrh2_seq": "ISSDVNDK", "cdrh3_seq": "AREQAVGTNPWAFDY", "cdrl1_seq": "QISSWGSDGKTY", "cdrl2_seq": "EVS", "cdrl3_seq": "MQGLHLPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 102]", "cdrh3_split": "val", "cdrh3_cluster": "8jn4", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DENV-290", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Envelope protein, Dengue virus type 3", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "HMAbs DENV-290 and DENV-115 potently neutralize DENV3 PSSP and CH53489 strains"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 14262, 17, 19029, 12, 20733, 1020, 1010, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 11262, 2213, 1927, 13304, 3413, 2601, 23, 18, 1920, 11262, 2213, 1977, 43, 4594, 1927, 1920, 4324, 3146, 5158, 2796, 1988, 4088, 1922, 19230, 5957, 1930, 28104, 1036, 1920, 4423, 3743, 2644, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 5985, 7644, 3413, 8576, 1942, 2094, 16, 2743, 2019, 1920, 4102, 1927, 1920, 47, 2213, 7632, 3436, 3418, 2890, 1927, 2288, 8179, 23583, 27306, 16, 11266, 43, 2814, 3347, 1021, 17, 45, 10095, 2921, 18, 3], "antigen": ["MRCVGVGNRDFVEGLSGATWVDVVLEHGGCVTTMAKNKPTLDIELQKTEATQLATLRKLCIEGKITNITTDSRCPTQGEAVLPEEQDQNYVCKHTYVDRGWGNGCGLFGKGSLVTCAKFQCLEPIEGKVVQYENLKYTVIITVHTGDQHQVGNETQGVTAEITPQASTTEAILPEYGTLGLECSPRTGLDFNEMILLTMKNKAWMVHRQWFFDLPLPWASGATTETPTWNRKELLVTFKNAHAKKQEVVVLGSQEGAMHTALTGATEIQNSGGTSIFAGHLKCRLKMDKLELKGMSYAMCTNTFVLKKEVSETQHGTILIKVEYKGEDAPCKIPFSTEDGQGKAHNGRLITANPVVTKKEEPVNIEAEPPFGESNIVIGIGDNALKINWYKKGSSIGKMFEATARGARRMAILGDTAWDFGSVGGVLNSLGKMVHQIFGSAYTALFSGVSWVMKIGIGVLLTWIGLNSKNTSMSFSCIAIGIITLYLGAVVQA"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A murine Fab, 237mAb (IGHV6/IGKV1-Kappa), targeting a tumor-specific glycosylated form of Podoplanin from Mus musculus. Podoplanin mediates effects on cell migration and adhesion through interactions with multiple partners, including roles in blood and lymphatic vessel separation, epithelial-mesenchymal transition, and invadopodia stability in tumor cells. The antibody is designed to recognize a glycopeptide epitope containing the Tn antigen (O-linked N-acetylgalactosamine) on Podoplanin with tumor specificity, achieving selectivity through combined recognition of both the glycan and peptide moieties. Please provide the HCDR sequences.", "target_protein": "QVQLQQSGGGLVQPGGSMKIFCAASMDWVRQSPEKGLEWVAEYYAESVKGRFTITRDDSKSRMSLQMNSLRAEDTGIYYCWGQGTTVTVSSKGFTFSDAWIRNKANNHETSGGKVRNAY", "metadata": {"pdb_id": "3iet", "light_chain_seq": "DIQLTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISSVEAEDLGVYFCSQSTHVPTFGGGTKLEIKRA", "cdrh1_seq": "GFTFSDAW", "cdrh2_seq": "IRNKANNHET", "cdrh3_seq": "SGGKVRNAY", "cdrl1_seq": "QSLVHSNGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "SQSTHVPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 106]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 100]", "cdrh3_split": "val", "cdrh3_cluster": "3iet", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "237mAb", "antibody_format": "Fab", "heavy_subclass": "IGHV6", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Podoplanin, Mus musculus", "target_domain": null, "functional_role": "other", "evidence_quote": "tumor-specific glycopeptide containing the Tn antigen"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 7135, 6914, 16, 20528, 3368, 1014, 12, 20733, 25606, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 43, 2798, 17, 2487, 17514, 2386, 1927, 10181, 3513, 15393, 2037, 3177, 25795, 1957, 18, 10181, 3513, 15393, 10412, 2564, 1990, 2024, 5049, 1930, 6141, 2596, 3719, 1956, 3137, 7228, 16, 2710, 5456, 1922, 2877, 1930, 13388, 8072, 7106, 16, 4944, 17, 9152, 4832, 16, 1930, 26908, 19597, 5057, 1922, 2798, 2094, 18, 1920, 3533, 1977, 4609, 1942, 9967, 43, 8821, 8253, 10095, 3165, 1920, 7417, 4730, 12, 57, 17, 4624, 56, 17, 6894, 5411, 2131, 17454, 13, 1990, 10181, 3513, 15393, 1956, 2798, 4896, 16, 11058, 9008, 2596, 4252, 5708, 1927, 2321, 1920, 15060, 1930, 4207, 16706, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["GTKPPL"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A murine Fab (IGHV1/IGKV4-Kappa) targeting Sulfhydryl oxidase 1 (QSOX1) of Mus musculus. Sulfhydryl oxidase 1 catalyzes the oxidation of sulfhydryl groups in peptide and protein thiols to disulfides and plays a role in disulfide bond formation in extracellular proteins, including laminin incorporation into the extracellular matrix. The antibody is designed to inhibit QSOX1 catalytic activity and reduce tumor cell migration through extracellular matrix organization.", "target_protein": "QVQLQQSGPELVKPGASVKISCKASIHWVKQRPGQGLEWIGWEYSEKFKGKATLTADTSSSTAYMQLSSLTSEDSAVYYCWGQGTLVTVSASGYSFTSYYIYPGSYNTARSEDWFAY", "metadata": {"pdb_id": "5d93", "light_chain_seq": "QIVLTQSPAIMSASPGEKVTISCSASSSVSYMYWYHQKPGSSPKPWIYRTSNLASGVPARFSGSGSGTSYSLTISSMEAEDAATYYCQQYHSYPLTFGAGTKLELKRT", "cdrh1_seq": "GYSFTSYY", "cdrh2_seq": "IYPGSYNT", "cdrh3_seq": "ARSEDWFAY", "cdrl1_seq": "SSVSY", "cdrl2_seq": "RTS", "cdrl3_seq": "QQYHSYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 104]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "5d93", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Sulfhydryl oxidase 1, Mus musculus", "target_domain": null, "functional_role": "other", "evidence_quote": "antibodies inhibit QSOX1 activity, decreased tumor cell migration"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 30011, 2199, 10488, 21, 12, 15178, 23599, 13, 1927, 3177, 25795, 1957, 18, 30011, 2199, 10488, 21, 17097, 1920, 6638, 1927, 30011, 2199, 2671, 1922, 4207, 1930, 2213, 27383, 1942, 11830, 1036, 1930, 5705, 43, 2770, 1922, 11830, 5403, 3337, 1922, 5329, 2697, 16, 2710, 15261, 8629, 2460, 1920, 5329, 4526, 18, 1920, 3533, 1977, 4609, 1942, 2875, 15178, 23599, 6804, 2455, 1930, 4412, 2798, 2024, 5049, 2596, 5329, 4526, 5901, 18, 3], "antigen": ["MSVLYSSSDPLTLLDADSVRPTVLGSSSAWAVEFFASWCGHCIAFAPTWKELANDVKDWRPALNLAVLDCAEETNSAVCREFNIAGFPTVRFFQAFTKNGSGATLPGAGANVQTLRMRLIDALESHRDTWPPACPPLEPAKLNDIDGFFTRNKADYLALVFEREDSYLGREVTLDLSQYHAVAVRRVLNTESDLVNKFGVTDFPSCYLLLRNGSVSRVPVLVESRSFYTSYLRGLPGLTR"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A human Fab, E7 (IGHV4/IGKV2-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a broadly neutralizing antibody capable of neutralizing diverse SARS-CoV-2 variants and cross-clade ACE2-dependent sarbecoviruses through recognition of a conserved quaternary epitope spanning the receptor-binding domain. Please generate its HCDRs.", "target_protein": "QVQLQESGPGLVKPSETLSLTCTVSWSWVRQPPGKGLEWIGYNYNPSLKSRLTISVDMSKSQFSLTLSSATAADTAVYYCWGQGTLVTVSSAGGFIGPHYIYISGSTARGGGYLETGPFEY", "metadata": {"pdb_id": "7y72", "light_chain_seq": "DIVMTQSPLSLPVTPGEPASISCRSSQSLLQNNGYNYLAWYLQKPGQSPQLLIYLSSTRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQSLQIPGTFGQGTRLEIKRT", "cdrh1_seq": "GGFIGPHY", "cdrh2_seq": "IYISGST", "cdrh3_seq": "ARGGGYLETGPFEY", "cdrl1_seq": "QSLLQNNGYNY", "cdrl2_seq": "LSS", "cdrl3_seq": "MQSLQIPGT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 108]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "7y72", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "E7", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "potent, broad-spectrum human monoclonal antibody capable of neutralizing all ACE2-binding sarbecoviruses"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 16325, 12, 20733, 1020, 1006, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 7131, 1927, 12130, 6445, 20466, 17, 6083, 17, 22, 4936, 1930, 3567, 17, 11315, 8298, 1028, 17, 3100, 9851, 12409, 18368, 2596, 5708, 1927, 43, 5305, 21920, 10095, 13346, 1920, 3148, 17, 2743, 3418, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["LCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNNCYFPLQSYGFQPTVGYQPYRVVVLSF", "LCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSF"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human Fab, p4-170 (IGHV3/IGLV1-Lambda), targeting the engineered Phosphate-binding protein PstS 1 of Mycobacterium tuberculosis H37Rv. PstS 1 is a phosphate-binding periplasmic protein that functions in inorganic phosphate uptake as part of the ABC transporter complex PstSACB and acts as a host TLR2 agonist that induces macrophage responses and mediates bacterial adhesion. The antibody is designed to restrict mycobacterial growth through Fc-dependent opsonization and antibody-mediated cellular uptake of bacteria via Fc\u03b3R engagement on macrophages. What would the HCDRs be?", "target_protein": "EVQLVESGGGLVKPGGSLRLSCAASMHWVRQAPGKGLEWVSSYYADSVKGRFTISRDNSGNSLFLQMNSLRVEDTAVYYCWGQGTLVTVSSAGFTFSSHRIISSRTYIARGDYYYDGVASDPHFDN", "metadata": {"pdb_id": "7dm2", "light_chain_seq": "SVLTQTPSASGTPGQRVTISCSGSRSNIGSNYVYWFQQFPGAAPQLLIYRNIQRPSGVPARFSGSKSDTSASLAISGLRSEDEAHYYCAAWDDSLSGVVFGGGTKVTVLGQ", "cdrh1_seq": "GFTFSSHR", "cdrh2_seq": "IISSRTYI", "cdrh3_seq": "ARGDYYYDGVASDPHFDN", "cdrl1_seq": "RSNIGSNY", "cdrl2_seq": "RNI", "cdrl3_seq": "AAWDDSLSGVV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[24, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "7dm2", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "p4-170", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "Phosphate-binding protein PstS 1, Mycobacterium tuberculosis H37Rv", "target_domain": null, "functional_role": "other", "evidence_quote": "mAbs mediate protection in vitro and in vivo via Fc-dependent opsonization"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 6914, 16, 9068, 17, 11222, 12, 20733, 1020, 1010, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 11091, 5413, 17, 2743, 2213, 16910, 1036, 21, 1927, 16389, 8449, 29253, 24895, 18, 16910, 1036, 21, 1977, 43, 5413, 17, 2743, 24334, 2213, 1988, 4088, 1922, 13849, 5413, 5047, 1966, 3131, 1927, 1920, 7219, 9054, 2796, 16910, 5735, 18598, 1930, 8016, 1966, 43, 4423, 15235, 7829, 1988, 6387, 8088, 3387, 1930, 10412, 4543, 6141, 18, 1920, 3533, 1977, 4609, 1942, 18240, 21424, 2905, 2596, 6437, 17, 3100, 26303, 2466, 1930, 3533, 17, 3434, 3689, 5047, 1927, 4802, 3454, 17536, 1005, 9577, 1990, 5205, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["TVATTPASSPVTLAETGSTLLYPLFNLWGPAFHERYPNVTITAQGTGSGAGIAQAAAGTVNIGASDAYLSEGDMAAHKGLMNIALAISAQQVNYNLPGVSEHLKLNGKVLAAMYQGTIKTWDDPQIAALNPGVNLPGTAVVPLHRSDGSGDTFLFTQYLSKQDPEGWGKSPGFGTTVDFPAVPGALGENGNGGMVTGCAETPGCVAYIGISFLDQASQRGLGEAQLGNSSGNFLLPDAQSIQAAAAGFASKTPANQAISMIDGPAPDGYPIINYEYAIVNNRQKDAATAQTLQAFLHWAITDGNKASFLDQVHFQPLPPAVVKLSDALIATISS"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A human Fab, ADI-15878 (IGHV3/IGKV1-Kappa), targeting the trimeric Envelope glycoprotein of Ebola virus. The Envelope glycoprotein forms virion surface spikes that mediate viral entry, with GP1 acting as the receptor-binding subunit and GP2 as the membrane fusion subunit. The antibody is designed as a pan-ebolavirus broadly neutralizing antibody that achieves broad neutralization across all five ebolavirus species by engaging conserved epitopes while bypassing species-specific polymorphisms in the GP2 N-terminal region.", "target_protein": "VQLVQSGVTLVQPGGSLRVSCAASMSWVRQAPGKGLEWVSAYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGALVTVSSAGFTFSSYAISGLGGSTAKDHRVWAAGYHFDY", "metadata": {"pdb_id": "6ea7", "light_chain_seq": "DIVLTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGEAPKLLISDASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYYSSPTFGGGTKVEIKTV", "cdrh1_seq": "GFTFSSYA", "cdrh2_seq": "ISGLGGST", "cdrh3_seq": "AKDHRVWAAGYHFDY", "cdrl1_seq": "QSISSW", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYYSSPT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6dzm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ADI-15878", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein, Ebola virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "pan-ebolavirus neutralizing human antibody capable of potently neutralizing all five ebolaviruses"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 2616, 6914, 16, 2041, 1033, 17, 14340, 7950, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 29177, 11262, 11424, 1927, 24497, 3413, 18, 1920, 11262, 11424, 4952, 19230, 3154, 14533, 1988, 8265, 4324, 6904, 16, 1956, 4882, 1009, 8290, 1966, 1920, 3148, 17, 2743, 5903, 1930, 4882, 1028, 1966, 1920, 3260, 5289, 5903, 18, 1920, 3533, 1977, 4609, 1966, 43, 3797, 17, 24497, 11074, 11984, 12130, 3533, 1988, 22665, 4949, 14377, 3436, 2136, 3628, 24497, 11074, 3038, 2007, 15888, 5305, 11427, 2679, 10344, 1941, 3038, 17, 2487, 8321, 1922, 1920, 4882, 1028, 56, 17, 4262, 3031, 18, 3], "antigen": ["AQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEP", "SIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAK", "PKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEP"]} {"modality_type": "antibody", "text": "A murine Fab, M8a-3 (IGHV1/IGKV6-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting a conserved class 1/4 epitope on the receptor-binding domain, with cross-reactive binding and neutralization across SARS-CoV-2 variants and animal sarbecoviruses. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "QVQLQQPGAELVLPGASVKLSCKASMHWVKQRPGHGLEWIGEKINQKFKGKSTLTVDTSSSTAYMQLSSLTSEDSAVYYCWGQGTTLTVSGYTFTNYWIDPFDTYIARPDSSGYPVYFDY", "metadata": {"pdb_id": "7uz4", "light_chain_seq": "DIVMTQSHKFMSTSVGDRVSITCKASQDVGTYIAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTNYTLTISSVQAEDLALYHCQQHYSTPYTFGGGTKLEI", "cdrh1_seq": "GYTFTNYW", "cdrh2_seq": "IDPFDTYI", "cdrh3_seq": "ARPDSSGYPVYFDY", "cdrl1_seq": "QDVGTY", "cdrl2_seq": "WAS", "cdrl3_seq": "QQHYSTPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7uz5", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "M8a-3", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "M8a-3 neutralized SARS-CoV-2 D614G with a 0.18 \u03bcg/mL IC50"}}}, "tokenized_instruction": [2, 43, 7135, 6914, 16, 55, 16269, 17, 23, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 43, 5305, 2921, 21, 19, 24, 10095, 1990, 1920, 3148, 17, 2743, 3418, 16, 1956, 3567, 17, 6079, 2743, 1930, 14377, 3436, 20466, 17, 6083, 17, 22, 4936, 1930, 4027, 9851, 12409, 18368, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["TQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A human Fab, F005-126 (IGHV1/IGLV1-Lambda), targeting the engineered Hemagglutinin of Influenza A virus (strain A/Hong Kong/1/1968 H3N2). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate virus attachment and entry, and undergoes low pH-induced conformational changes in endosomes to facilitate membrane fusion. The antibody is designed as a neutralizing antibody that stabilizes the HA head and prevents the low pH-induced conformational transition to the postfusion state, thereby blocking virus entry.", "target_protein": "QVQLVQSGAEVKKPGASVTVSCQVSLSWVRQAPGQGLEWVGWKYVKKFQGRVTMTTHTGTNTAYMEMKSLRSDDTAVYYCWGQGTMVTVSSKGYTLTSYGINTYDGQTARVEGVRGVMGFHYYPMDV", "metadata": {"pdb_id": "7k39", "light_chain_seq": "SVLTQPPSVSGAPGQRVTISCTGSSAVHWYQQLPGTAPKLLISGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSSVFGGGTKLTVLGR", "cdrh1_seq": "GYTLTSYG", "cdrh2_seq": "INTYDGQT", "cdrh3_seq": "ARVEGVRGVMGFHYYPMDV", "cdrl1_seq": "SA", "cdrl2_seq": "GNS", "cdrl3_seq": "QSSV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[24, 25]", "cdrl2_pos": "[43, 45]", "cdrl3_pos": "[82, 85]", "cdrh3_split": "val", "cdrh3_cluster": "3whe", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "F005-126", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus (strain A/Hong Kong/1/1968 H3N2)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody targeting the HA head; prevents low pH-induced conformational transition to postfusion state"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 2616, 6914, 16, 17930, 15264, 17, 10483, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 11091, 26141, 1927, 7108, 43, 3413, 12, 3943, 43, 19, 15908, 18143, 19, 21, 19, 22553, 25234, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 3413, 8576, 1930, 6904, 16, 1930, 14928, 2330, 2087, 17, 2719, 8523, 2840, 1922, 14978, 1942, 6628, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 19658, 1920, 2118, 4469, 1930, 10299, 1920, 2330, 2087, 17, 2719, 8523, 4832, 1942, 1920, 2753, 9049, 3360, 16, 6113, 7472, 3413, 6904, 18, 3], "antigen": ["STATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEK", "GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQ"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human Fab, COVA2-15 (IGHV3/IGKV2-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting the Receptor-binding domain (RBD), with binding capacity to all three RBD domains in the down conformation of the trimeric spike. Can you generate its HCDRs?", "target_protein": "QVQLLESGGGLVQPGGSLRLSCAASMSWVRQAPGKGLEWASAYYADSVEGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTFSSYAISGSGGSTAKDTGYCGDDCYIKLIRGGPDY", "metadata": {"pdb_id": "9b82", "light_chain_seq": "DIVMTQSPLSLPVTLGQPASISCRSSQSLVYSDGNTFLNWFQQRPGQSPRRLIYQVSNRDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQGTHWPRTFGQGTKLEIKRT", "cdrh1_seq": "GFTFSSYA", "cdrh2_seq": "ISGSGGST", "cdrh3_seq": "AKDTGYCGDDCYIKLIRGGPDY", "cdrl1_seq": "QSLVYSDGNTF", "cdrl2_seq": "QVS", "cdrl3_seq": "MQGTHWPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 117]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "9b82", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "COVA2-15", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV2", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "COVA2-15 with very high neutralization potency"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 6914, 16, 6083, 8398, 17, 2461, 12, 20733, 1020, 1010, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 1956, 2743, 4796, 1942, 2136, 2559, 25780, 4682, 1922, 1920, 3292, 7748, 1927, 1920, 29177, 10429, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A human Fab, 447-52D (IGHV3/IGLV1-Lambda), targeting the V3 loop of the Envelope glycoprotein of Human immunodeficiency virus 1. The antibody is designed as a broadly neutralizing antibody capable of recognizing V3 peptides containing both GPGR and GPGQ crown motifs across multiple HIV-1 clades. The design should accommodate an elongated CDR H3 that engages the V3 crown through main-chain interactions and a binding site architecture that tolerates sequence variation while maintaining neutralizing capacity.", "target_protein": "EVQLVESGGGLVKPGGSLRLTCVASLNWVRQAPGKGLEWVGRDYAASVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYSCWGKGTTVTVSSAGFTFSDVWIKSRTDGGTTTTDGFIMIRGVSEDYYYYYMDV", "metadata": {"pdb_id": "3ghb", "light_chain_seq": "QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVLWYQQFPGTAPKLLIYGNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYFCATWDSGLSADWVFGGGTKLTVLSQ", "cdrh1_seq": "GFTFSDVW", "cdrh2_seq": "IKSRTDGGTT", "cdrh3_seq": "TTDGFIMIRGVSEDYYYYYMDV", "cdrl1_seq": "SSNIGNNY", "cdrl2_seq": "GNN", "cdrl3_seq": "ATWDSGLSADWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 119]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 100]", "cdrh3_split": "val", "cdrh3_cluster": "4m1d", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "447-52D", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein, Human immunodeficiency virus 1", "target_domain": "V3 loop", "functional_role": "neutralizing", "evidence_quote": "broadly reactive with V3 containing both the GPGR and GPGQ crown motifs"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 29146, 17, 4764, 1007, 12, 20733, 1020, 1010, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 14307, 5881, 1927, 1920, 11262, 11424, 1927, 2616, 13141, 3413, 21, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 7131, 1927, 15667, 14307, 5320, 3165, 2321, 4882, 2299, 1930, 4882, 1029, 1055, 18819, 8277, 3436, 3137, 3525, 17, 21, 15961, 18, 1920, 3036, 3066, 16848, 1925, 16158, 20170, 8170, 1988, 11580, 1036, 1920, 14307, 18819, 2596, 2730, 17, 4659, 3719, 1930, 43, 2743, 3200, 9335, 1988, 21407, 1036, 3244, 4516, 2679, 8231, 12130, 4796, 18, 3], "antigen": ["KGVRIGPGQA"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, CH04 (IGHV3/IGKV3-Kappa), targeting the V1V2 domain of the Envelope glycoprotein gp160 of Human immunodeficiency virus type 1. The gp160 precursor is proteolytically cleaved to produce gp120, which attaches the virus to the host lymphoid cell by binding to the primary receptor CD4 and induces structural rearrangement creating a high-affinity binding site for chemokine coreceptors. The antibody is designed as a broadly neutralizing antibody targeting the V1V2 domain, which requires recognition of quaternary glycan epitopes and strand-strand interactions with the V1V2 C strand, with a long anionic CDR H3 capable of penetrating the glycan shield to engage the underlying protein epitope.", "target_protein": "EVQLVESGGGLIRPGGSLRLSCKGSFGWVRQGPGKGLEWVSGRYGDSVKGRFTISRDNSNNFVYLQMNSLRPEDTAIYYCWGRGTLVTVSSAGFIFENFGTNWNGGDSARGTDYTIDDQGIRYQGSGTFWYFDV", "metadata": {"pdb_id": "5esz", "light_chain_seq": "EIVLTQSPDTLSLSPGERATLSCRASSSRYFAWYQHKPGQPPRLLIYGGSTRATGIPNRFSAGGSGTQFTLTVNRLEAEDFAVYYCQQYGRSPYTFGQGTKVEIRRT", "cdrh1_seq": "GFIFENFG", "cdrh2_seq": "TNWNGGDS", "cdrh3_seq": "ARGTDYTIDDQGIRYQGSGTFWYFDV", "cdrl1_seq": "SSRY", "cdrl2_seq": "GGS", "cdrl3_seq": "QQYGRSPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 121]", "cdrl1_pos": "[26, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "5esz", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CH04", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus type 1", "target_domain": "Human immunodeficiency virus 1 envelope glycoprotein Gp120 V1V2 domain", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibodies (bNAbs) against HIV-1-Env V1V2"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 2016, 14743, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11217, 15755, 3418, 1927, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 2601, 21, 18, 1920, 4882, 16954, 7897, 1977, 12712, 2169, 10246, 1942, 5074, 16102, 16, 2154, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 1930, 6387, 4346, 14154, 11124, 43, 2149, 17, 5173, 2743, 3200, 1958, 11673, 30435, 3448, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 11217, 15755, 3418, 16, 2154, 5474, 5708, 1927, 21920, 15060, 11427, 1930, 5984, 17, 5984, 3719, 1956, 1920, 11217, 15755, 45, 5984, 16, 1956, 43, 2815, 19696, 20170, 8170, 7131, 1927, 19879, 1920, 15060, 19397, 1942, 11580, 1920, 5030, 2213, 10095, 18, 3], "antigen": ["SLIRIGHGFDVHCVTLHCTNNCSFNMTTELRDKKQKVHALFYKLDIVPINSKYRLIGGSGGDVALHALTDAILGAAALGDIGKLFPKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATGIACEAVALLIRQ"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A human Fab, MF3178 (IGHV1/IGKV1-Kappa), targeting the engineered ectodomain of Receptor tyrosine-protein kinase erbB-3 (HER3). HER3 is a tyrosine-protein kinase that acts as a cell surface receptor for neuregulins, binding neuregulin-1 to activate phosphatidylinositol 3-kinase signaling and promote cell survival. The antibody is designed to inhibit HER3 signaling and downstream PI3K/Akt pathway activation, functioning as part of a bispecific antibody strategy to block heregulin-mediated HER3 activation in HER2-driven cancers.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASMHWVRQAPGQGLEWMGWNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCWGQGTLVTVSSAGYTFTGYYINPNSGGTARDHGSRHFWSYWGFDY", "metadata": {"pdb_id": "5o7p", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPTFGQGTKVEIKRT", "cdrh1_seq": "GYTFTGYY", "cdrh2_seq": "INPNSGGT", "cdrh3_seq": "ARDHGSRHFWSYWGFDY", "cdrl1_seq": "QSISSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSYSTPPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5o4o", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Receptor tyrosine-protein kinase erbB-3, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "potently inhibits the HRG/HER3 pathway and downstream PI3K/Akt signaling"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 2616, 6914, 16, 8168, 6800, 7950, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 27385, 1927, 3148, 6941, 17, 2213, 4016, 11954, 17, 23, 12, 3656, 1010, 13, 18, 3656, 1010, 1977, 43, 6941, 17, 2213, 4016, 1988, 8016, 1966, 43, 2024, 3154, 3148, 1958, 2974, 6541, 19962, 16, 2743, 2974, 6541, 3392, 17, 21, 1942, 6980, 16927, 23, 17, 4016, 3197, 1930, 5527, 2024, 3298, 18, 1920, 3533, 1977, 4609, 1942, 2875, 3656, 1010, 3197, 1930, 5863, 7734, 19, 5496, 3374, 2936, 16, 7295, 1966, 3131, 1927, 43, 7266, 10231, 3533, 4884, 1942, 3367, 3410, 11056, 7782, 17, 3434, 3656, 1010, 2936, 1922, 9162, 17, 6446, 5717, 18, 3], "antigen": ["QAVCPGTRCEVVMGNLEIVLTGHNADLSFLQWIREVTGYVLVAMNEFSTLPLPNLRVVRGTQVYDGKFAIFVMLNYNTNSSHALRQLRLTQLTEILSGGVYIEKNDKLCHMDTIDWRDIVRDRDAEIVVKDNGRSCPPCHEVCKGRCWGPGSEDCQTLTKTICAPQCNGHCFGPNPNQCCHDECAGGCSGPQDTDCFACRHFNDSGACVPRCPQPLVYNKLTFQLEPNPHTKYQYGGVCVASCPHNFVVDQTSCVRACPPDKMEVDKNGLKMCEPCGGLCPKACEGTGSGSRFQTVDSSNIDGFVNCTKILGNLDFLITGLNGDPWHKIPALDPEKLNVFRTVREITGYLNIQSWPPHMHNFSVFSNLTTIGGRSLYNRGFSLLIMKNLNVTSLGFRSLKEISAGRIYISANRQLCYHHSLNWTKVLRGPTEERLDIKHNRPRRDCVAEGKVCDPLCSSGGCWGPGPGQCLSCRNYSRGGVCVTHCNFLNGEPREFAHEAECFSCHPECQPMEGTATCNGSGSDTCAQCAHFRDGPHCVSSCPHGVLGAKGPIYKYPDVQNECRPCHENCTQGCKGPELQDC"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that engages the receptor-binding domain and recognizes a conserved glycan-containing epitope within the Sarbecovirus subgenus without competing with receptor attachment.", "target_protein": "VQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "6wpt", "light_chain_seq": "IVLTQSLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVE", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 114]", "cdrl1_pos": "[22, 28]", "cdrl2_pos": "[46, 48]", "cdrl3_pos": "[83, 90]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 11580, 1036, 1920, 3148, 17, 2743, 3418, 1930, 16197, 43, 5305, 15060, 17, 3165, 10095, 2651, 1920, 9851, 12409, 7414, 22374, 1957, 2979, 11743, 1956, 3148, 8576, 18, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVNCTFEYVSFKNLREFVFKNIDGYFKIYSKHTPINLRDLPQGFSALEPLVDLPIGINITRFQTLLAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKNYNYLYRKPFERDISTPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKSKRSFIEDLLFNKVTNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A murine Fab, H263.A2 (IGHV1/IGKV12-Kappa), targeting the Major capsid protein L1 of Human papillomavirus type 16. The L1 protein forms an icosahedral capsid with T=7 symmetry and binds to heparan sulfate proteoglycans on cell surfaces to mediate initial virion attachment, triggering conformational changes that facilitate infection. The antibody is designed as a neutralizing antibody that stabilizes the L1 capsomer by engaging multiple loops from different L1 proteins.", "target_protein": "LQQSGAELARPGASVKLSCKASMQWVKQRPGQGLEWIGARYTQKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYYCWGQGTLVTVSGYTFISYWIYPGDGATARPSYYDYDVTWFAY", "metadata": {"pdb_id": "3j8w", "light_chain_seq": "DIVMTQTPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAETLAEGVPSRFSGSGSGTQFSLRINSLQPEDFGSYYCQHHYVSPLTFGAGTKLELKRA", "cdrh1_seq": "GYTFISYW", "cdrh2_seq": "IYPGDGAT", "cdrh3_seq": "ARPSYYDYDVTWFAY", "cdrl1_seq": "ENIYSY", "cdrl2_seq": "NAE", "cdrl3_seq": "QHHYVSPLT", "cdrh1_pos": "[22, 29]", "cdrh2_pos": "[47, 54]", "cdrh3_pos": "[93, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3j8w", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "H263.A2", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV12", "is_engineered": false, "target_antigen": "Major capsid protein L1, Human papillomavirus type 16", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing monoclonals (mAbs): H16.1A, H16.14J, and H263.A2"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 7135, 6914, 16, 4881, 7576, 18, 8595, 12, 20733, 7390, 19, 7021, 1040, 7390, 1028, 17, 12093, 13, 16, 5133, 1920, 3044, 14681, 2213, 7554, 1927, 2616, 22474, 2601, 2641, 18, 1920, 7554, 2213, 4952, 1925, 29310, 24704, 14681, 1956, 62, 33, 27, 12572, 1930, 6876, 1942, 22024, 8767, 25185, 1990, 2024, 7553, 1942, 8265, 3754, 19230, 8576, 16, 14074, 8523, 2840, 1988, 6628, 2909, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 19658, 1920, 7554, 7070, 4528, 2007, 15888, 3137, 11109, 2037, 2413, 7554, 2697, 18, 3], "antigen": ["AVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPLLNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTQVAVQPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGTVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQLGL"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A rhesus macaque Fab, CHM-27 (IGHV1/IGLV1-Lambda), targeting the stem helix peptide of the Spike glycoprotein of Middle East respiratory syndrome-related coronavirus. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host DPP4 receptor and mediates fusion of viral and cellular membranes through conformational transitions from pre-fusion to post-fusion hairpin states. The antibody is designed as a neutralizing antibody targeting the stem helix region.", "target_protein": "VQLVQSGTEIKQPGASVKLSCKASIHWVRQAPGQGLEWIGLVYPQSFQGRVIMTTDTSTSTAFLDLHSLRSEDTAVYYCWGPGVLVTVSSAGYTFSSDYISPQSGNKTRGRLDV", "metadata": {"pdb_id": "8tmz", "light_chain_seq": "SVLTQPPSVSAAPGQKVTISCSGSSSNIARSYVSWHHHVPGTAPKVLIYGTNNRPSGVSDRFSGSKSGTSAFLAITGLQTGDEGDYYCGTWDTSLSAVLFGGGTRLTVLGQ", "cdrh1_seq": "GYTFSSDY", "cdrh2_seq": "ISPQSGNK", "cdrh3_seq": "TRGRLDV", "cdrl1_seq": "SSNIARSY", "cdrl2_seq": "GTN", "cdrl3_seq": "GTWDTSLSAVL", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 101]", "cdrl1_pos": "[24, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "8tmz", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CHM-27", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "Stem helix peptide of Spike glycoprotein, Middle East respiratory syndrome-related coronavirus", "target_domain": "stem helix", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 16996, 20533, 6914, 16, 2016, 1035, 17, 3225, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 4402, 7864, 4207, 1927, 1920, 10429, 11424, 1927, 5576, 10319, 5481, 4741, 17, 2712, 5548, 10703, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 16423, 1006, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 10673, 2037, 2097, 17, 5289, 1942, 2753, 17, 5289, 14565, 4376, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 4402, 7864, 3031, 18, 3], "antigen": ["GIDFQDELDEFFKNV"]} {"modality_type": "antibody", "text": "Output the HCDRs for an antibody that performs this function: A rhesus macaque Fab, K11 (IGHV4/IGKV1-Kappa), targeting the Envelope glycoprotein gp120 of Simian immunodeficiency virus. The gp120 surface protein attaches the virus to the host lymphoid cell by binding to the primary receptor CD4, inducing structural rearrangement that creates a high-affinity binding site for a chemokine coreceptor, and also targets the virus to gut-associated lymphoid tissue by binding host integrins. The antibody is designed as a neutralizing antibody targeting the glycan hole epitope, a conserved neutralizing site on the trimeric Env that depends on sub-occupancy at specific N-linked glycosylation sites.", "target_protein": "QLQESGPGVVRPSQTLSLTCAVSWTWIRQPPGKGLEWIGNNYNPSLKTRISISKDMSKNQFSLKLNSLTATDTAIYYCWGQGVLVTVSSGDTVSSCCFFIYSDNDNTARESPSRGNFCYAYLYGNCPLHFDL", "metadata": {"pdb_id": "7t4g", "light_chain_seq": "DILLTQSPSSLSGSVGDRVTITCRASQGINSYLNWYQQKPGKAPKLLIYFANRLQSGVPSRFSGSGSGTEFTLTISSLQSEDGATYYCQQYDTFPTFGPGTKLDIK", "cdrh1_seq": "GDTVSSCCFF", "cdrh2_seq": "IYSDNDNT", "cdrh3_seq": "ARESPSRGNFCYAYLYGNCPLHFDL", "cdrl1_seq": "QGINSY", "cdrl2_seq": "FAN", "cdrl3_seq": "QQYDTFPT", "cdrh1_pos": "[23, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 120]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "7t2p", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "K11", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp120, Simian immunodeficiency virus", "target_domain": "glycan hole", "functional_role": "neutralizing", "evidence_quote": "K11 neutralized SIVmac239 at an IC50 of 0.12 \u03bcg/mL and protected rhesus macaques from repeated SIVmac239 challenge"}}}, "tokenized_instruction": [2, 6647, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 17436, 2052, 2347, 30, 43, 16996, 20533, 6914, 16, 16185, 1009, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 16102, 1927, 30130, 13141, 3413, 18, 1920, 16102, 3154, 2213, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1988, 15628, 43, 2149, 17, 5173, 2743, 3200, 1958, 43, 11673, 30435, 2684, 16, 1930, 2222, 4845, 1920, 3413, 1942, 7660, 17, 2458, 11751, 2960, 2007, 2743, 4423, 15563, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 15060, 13356, 10095, 16, 43, 5305, 12130, 3200, 1990, 1920, 29177, 11118, 1988, 7315, 1990, 2316, 17, 13771, 2019, 2487, 56, 17, 4624, 12082, 3402, 18, 3], "antigen": ["TLYVTVFYGVPAWRNATIPLFCATKNRDTWGTTQCLPDNGDYSEMALNVTESFDAWNNTVTEQAIEDVWQLFETSIKPCVKLSPLCITMRCNKSETDRWGLTKSITTTASTTSTTASAKVDMVNETSSCIAQDNCTGLEQEQMISCKFNMTGLKRDKSKEYNETWYSADLVCEQGNNTGNESRCYMNHCNTSVIQESCDKHYWDAIRFRYCAPPGYALLRCNDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFNGTRAENRTYIYWHGRDNRTIISLNKYYNLTMKCRRPGNKTVLPVTIMSGLVFHSQPINDRPKQAWCWFGGKWKDAIKEVKQTIVKHPRYTGTNNTDKINLTAPGGGDPEVTFMWTNCRGEFLYCKMNWFLNWVEDRNTANQKPKEQHKRNYVPCHIRQIINTWHKVGKNVYLPPREGDLTCNSTVTSLIANIDWIDGNQTNITMSAEVAELYRLELGDYKLVEITPIGLAPTSCKRY"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A single-chain Fv (scFv), 2-7 (IGHV2/IGLV6-Lambda), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptor ACE2, initiating infection, and mediates fusion of the virion and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting the conserved receptor-binding domain core, with the objective of maintaining neutralization breadth against circulating variants of concern.", "target_protein": "QVTLKESGPTRVKPTQTLTLTCTFSVGWIRQPPGKALEWLALRYSPSLKSRLTITKDTSKNQVVLTMTNMDPVDTATYYCWGQGTTVTVSSGFSLSTTGVGIYWNDDKARISGSGYFYPFDI", "metadata": {"pdb_id": "7t3m", "light_chain_seq": "FMLTQPHSVSESPGKTVTISCTRSSGSIASNYVQWYQQRPGSSPTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISGLKAEDEADYYCQSYDSSSLWVFGGGTKLTVL", "cdrh1_seq": "GFSLSTTGVG", "cdrh2_seq": "IYWNDDK", "cdrh3_seq": "ARISGSGYFYPFDI", "cdrl1_seq": "SGSIASNY", "cdrl2_seq": "EDN", "cdrl3_seq": "QSYDSSSLWV", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 110]", "cdrl1_pos": "[24, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[90, 99]", "cdrh3_split": "val", "cdrh3_cluster": "7t3m", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2-7", "antibody_format": "scFv", "heavy_subclass": "IGHV2", "light_subclass": "IGLV6", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing anti-SARS-CoV-2 antibodies that target non-overlapping epitopes"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2957, 17, 4659, 11417, 12, 19863, 13, 16, 22, 17, 27, 12, 20733, 15755, 19, 28961, 25606, 17, 18279, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 3148, 8298, 1028, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 1920, 19230, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 5305, 3148, 17, 2743, 3418, 4728, 16, 1956, 1920, 4470, 1927, 8231, 14377, 22532, 3316, 7396, 4936, 1927, 8353, 18, 3], "antigen": ["PAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLMESEFRVYSSANNCTFEYVSQPFLMFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFK"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab, CV2-75 (IGHV4/IGLV3-Lambda), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the host cell membrane by interacting with ACE2 and other receptors, initiating infection and mediating fusion of viral and cellular membranes. The antibody is designed as a neutralizing antibody that blocks ACE2 binding to the RBD and cross-neutralizes SARS-CoV-1 and the B.1.351 variant, binding within the Receptor-binding domain (RBD) at an epitope distinct from the receptor-binding motif. Please output the HCDRs.", "target_protein": "VQLQESGPGLVKPSETLSLTCTVSWSWIRQPPGKGLEWIGYNYNPSLKSRVTISVDTSKNEFSLKLSSVTAADTAVYYCWGQGTLVTVSSAGGSISSYYVYYSGSTASSQRPDGNLYYFDY", "metadata": {"pdb_id": "7m3i", "light_chain_seq": "SYVLTQPPSVSVAPGQTARITCGGNNIGSKTVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHYVFGTGTKVTVLGQ", "cdrh1_seq": "GGSISSYY", "cdrh2_seq": "VYYSGST", "cdrh3_seq": "ASSQRPDGNLYYFDY", "cdrl1_seq": "NIGSKT", "cdrl2_seq": "DDS", "cdrl3_seq": "QVWDSSSDHYV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 55]", "cdrh3_pos": "[94, 108]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 97]", "cdrh3_split": "val", "cdrh3_cluster": "7m3i", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CV2-75", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "CV2-75 neutralizes SARS-CoV-2 and SARS-CoV-1 and retains neutralizing activity against B.1.351"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 5519, 1028, 17, 4089, 12, 20733, 1020, 1006, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 8298, 1028, 1930, 2303, 4086, 16, 12410, 2909, 1930, 10239, 5289, 1927, 4324, 1930, 3689, 5726, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 8298, 1028, 2743, 1942, 1920, 25780, 1930, 3567, 17, 25885, 1036, 20466, 17, 6083, 17, 21, 1930, 1920, 44, 18, 21, 18, 26247, 6031, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 2019, 1925, 10095, 4493, 2037, 1920, 3148, 17, 2743, 5219, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNK"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab, Z2B3 (IGHV1/IGLV2-Lambda), targeting the Neuraminidase of Influenza A virus (H7N9). Neuraminidase catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates, facilitating virus release and spread through the circulation. The antibody is designed as a broadly neutralizing antibody that inhibits neuraminidase enzymatic activity and confers protection against diverse influenza strains, binding within the Head of neuraminidase at the conserved active site.", "target_protein": "VQLVQSGAEVKKPGSSVKVSCKASFSWVRQAPGQGLEWMGGNYAQKFQGRVTITADESTSTAYMELSSLKSEDTAVYYCWGQGTTVTVSSAGGPFSSYGIIPVYGTTARDLQDTPMVDRIIGSYYYYNGLDV", "metadata": {"pdb_id": "6lxj", "light_chain_seq": "SVLTQPASVSGSPGQSITISCTGASSDYNYVSWYQQHPGKAPKLMIYDVSNRPSGVSNRFSGSKSGDTASLTISGLQAEDEADYYCSSYTRSSSVVFGGGTKLTVLGQ", "cdrh1_seq": "GGPFSSYG", "cdrh2_seq": "IIPVYGTT", "cdrh3_seq": "ARDLQDTPMVDRIIGSYYYYNGLDV", "cdrl1_seq": "SSDYNY", "cdrl2_seq": "DVS", "cdrl3_seq": "SSYTRSSSVV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 119]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6lxj", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Z2B3", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Neuraminidase, Influenza A virus (A/Anhui/1-BALF_RG44/2013(H7N9))", "target_domain": "Head of neuraminidase", "functional_role": "neutralizing", "evidence_quote": "cross-inhibition and protection against seasonal H1N1, H5N1, and H7N9 viruses"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 16, 68, 9385, 1010, 12, 20733, 7390, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 29831, 1927, 7108, 43, 3413, 12, 16754, 28955, 13, 18, 29831, 17097, 1920, 6025, 1927, 4262, 20436, 2687, 4248, 2037, 4324, 1930, 3689, 4235, 30378, 2209, 16, 12440, 3413, 4012, 1930, 6441, 2596, 1920, 9255, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1988, 7042, 29831, 8145, 2455, 1930, 16556, 6202, 3316, 6445, 7108, 4046, 16, 2743, 2651, 1920, 4469, 1927, 29831, 2019, 1920, 5305, 3500, 3200, 18, 3], "antigen": ["RNFNNLTKGLCTINSWHIYGKDNAVRIGESSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKSRMSICISGPNNNASAVVWYNRRPVAEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPADTRIYYFKEGKILKWESLTGTAKHIEECSCYGERTGITCTCRDNWQGSNRPVIQIDPVAMTHTSQYICSPVLTDNPRPNDPNIGKCNDPYPGNNNNGVKGFSYLDGANTWLGRTISTASRSGYEMLKVPNALTDDRSKPIQGQTIVLNADWSGYSGSFMDYWAEGDCYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWNWPDGAKIEYFL"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A murine Fv, mAb6D8 (IGHV14/IGKV3-Kappa), targeting Merozoite surface protein 2 (MSP2) of Plasmodium falciparum. MSP2 may play a role in merozoite attachment to the erythrocyte and is an intrinsically disordered, membrane-anchored antigen of the malaria parasite. The antibody is designed to recognize a conserved N-terminal epitope of MSP2 on the parasite surface, with the objective of engaging MSP2 in a conformation compatible with its membrane-bound state rather than the unstructured solution form.", "target_protein": "QVQLQQSGDELVKPGASVKLSCTVSIHWMKQRPEQGLEWIGRKYAPKFQDKATMTADTSSNTAYLQLSSLASEDAAVYYCWGQGTLVTVSAGFNIKDDFIDPANGYTATYGVAY", "metadata": {"pdb_id": "4r3s", "light_chain_seq": "DIVLTQSPASLAVSLGQRATISCKASQSVDHDGDSYMNWFQQKPGQSPKLLIYAASNLESGIPARFSGSGSGTDFTLNIHPVEEEDAATYYCQQTNEDPYTFGGGTKLEIK", "cdrh1_seq": "GFNIKDDF", "cdrh2_seq": "IDPANGYT", "cdrh3_seq": "ATYGVAY", "cdrl1_seq": "QSVDHDGDSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQTNEDPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 102]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "4r3s", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "mAb6D8", "antibody_format": "Fv", "heavy_subclass": "IGHV14", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Merozoite surface protein 2, Plasmodium falciparum", "target_domain": null, "functional_role": "other", "evidence_quote": "antibodies able to recognize the N-terminal region of MSP2 on the merozoite surface"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 7135, 11417, 16, 7032, 1016, 1007, 1025, 12, 20733, 7390, 1006, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 6902, 26553, 3154, 2213, 22, 12, 22064, 1028, 13, 1927, 15663, 13098, 18, 22064, 1028, 2278, 3918, 43, 2770, 1922, 6902, 26553, 8576, 1942, 1920, 15469, 1930, 1977, 1925, 20061, 13885, 16, 3260, 17, 17199, 4730, 1927, 1920, 7505, 8652, 18, 1920, 3533, 1977, 4609, 1942, 9967, 43, 5305, 56, 17, 4262, 10095, 1927, 22064, 1028, 1990, 1920, 8652, 3154, 16, 1956, 1920, 4470, 1927, 15888, 22064, 1028, 1922, 43, 7748, 11290, 1956, 2496, 3260, 17, 4124, 3360, 4356, 2254, 1920, 23572, 3331, 2386, 18, 3], "antigen": ["INNAYNMSIRRS"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human Fab, Fab356 (IGHV3/IGKV3-Kappa), targeting the NPNA2 peptide epitope from the Circumsporozoite protein of Plasmodium falciparum. The Circumsporozoite protein is an essential sporozoite protein required for sporozoite migration through the host dermis and infection of host hepatocytes, binding to highly sulfated heparan sulfate proteoglycans on hepatocyte surfaces. The antibody is designed to confer protection against malaria parasites in the liver stage of infection, with binding affinity to longer NPNA repeat peptides (NPNA4 and NPNA6) correlating with in vivo parasite burden reduction. Generate the corresponding HCDRs.", "target_protein": "VQLVESGGGVVQPGRSLRLSCAASMHWVRQTPGKGLEWVAVFYADSVEGRFTISRDNSKNMIYLQMNSLRVEDTAIYYCWGQGTLVTVSSAGFTFRNFGIWHDGSNKARDSLFYDHDNSGYYGY", "metadata": {"pdb_id": "6w05", "light_chain_seq": "QIVMTQSPATVSVSPGERATLSCRASRSVTSKLAWYQQKPGQAPRLLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAVYFCQQYNNGFTFGPGTKVDFKRT", "cdrh1_seq": "GFTFRNFG", "cdrh2_seq": "IWHDGSNK", "cdrh3_seq": "ARDSLFYDHDNSGYYGY", "cdrl1_seq": "RSVTSK", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYNNGFT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 111]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6w05", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Fab356", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Circumsporozoite protein, Plasmodium falciparum", "target_domain": null, "functional_role": "other", "evidence_quote": "antibody in vivo protection correlates with Fab apparent affinity; inhibited parasite liver burden load"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 6914, 16, 6914, 5798, 1016, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 5007, 2175, 1028, 4207, 10095, 2037, 1920, 28868, 2074, 26553, 2213, 1927, 15663, 13098, 18, 1920, 28868, 2074, 26553, 2213, 1977, 1925, 4415, 9130, 26553, 2213, 3414, 1958, 9130, 26553, 5049, 2596, 1920, 4423, 20201, 1930, 2909, 1927, 4423, 9919, 16, 2743, 1942, 3626, 26649, 22024, 8767, 25185, 1990, 14675, 7553, 18, 1920, 3533, 1977, 4609, 1942, 7909, 6202, 3316, 7505, 9687, 1922, 1920, 3568, 3587, 1927, 2909, 16, 1956, 2743, 5173, 1942, 4872, 5007, 2175, 6865, 5320, 12, 5007, 2175, 1006, 1930, 5007, 2175, 1016, 13, 20117, 1956, 1922, 3597, 8652, 6700, 3378, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["NPNANPNA"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A human Fab, Z13e1 (IGHV4/IGKV3D-Kappa), targeting Interleukin-22 of Homo sapiens. Interleukin-22 is a cytokine that plays a critical role in modulating tissue responses during inflammation and in the regeneration of epithelial cells to maintain barrier function after injury. This antibody is intended as a structural tool for use as a reagent to detect Z13e1-like antibodies through an engineered epitope-display scaffold protein containing the HIV-1 gp41 MPER epitope grafted onto the IL-22 framework.", "target_protein": "EVQLLESGPGLLKPSETLSLTCTVSWSWIRQPPGERPQWLGHKYNPSLESRITISRDISKNQFSLRLNSVTAADTAIYYCWGSGTAVTVSSAGGSMINYYIIYGGTTARVAIGVSGFLNYYYYMDV", "metadata": {"pdb_id": "3q1s", "light_chain_seq": "ELTQSPATLSLSPGERATLSCRASQSVGRNLGWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQARLLLPQTFGQGTKVEIKRT", "cdrh1_seq": "GGSMINYY", "cdrh2_seq": "IIYGGTT", "cdrh3_seq": "ARVAIGVSGFLNYYYYMDV", "cdrl1_seq": "QSVGRN", "cdrl2_seq": "DAS", "cdrl3_seq": "QARLLLPQT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 113]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "3q1s", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Z13e1", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV3D", "is_engineered": false, "target_antigen": "Interleukin-22, Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "epitope display protein for detection of Z13e1-like antibodies"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 2616, 6914, 16, 68, 3633, 12474, 12, 20733, 1020, 1006, 19, 7021, 1040, 1020, 19494, 17, 12093, 13, 16, 5133, 9198, 17, 2950, 1927, 16350, 27974, 18, 9198, 17, 2950, 1977, 43, 6137, 1988, 5705, 43, 4140, 2770, 1922, 10871, 2960, 3387, 2409, 4531, 1930, 1922, 1920, 8596, 1927, 4944, 2094, 1942, 6698, 7104, 2347, 2256, 4047, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1958, 2485, 1966, 43, 7916, 1942, 4277, 68, 3633, 12474, 17, 3189, 3788, 2596, 1925, 11091, 10095, 17, 4434, 7281, 2213, 3165, 1920, 3525, 17, 21, 25618, 5438, 1915, 10095, 19168, 6131, 1920, 2614, 17, 2950, 6465, 18, 3], "antigen": ["CRLDKSNMLAKEAWNWDDITDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human Fab, HBC34 (IGHV3/IGLV3-Lambda), targeting the Middle S protein of Hepatitis B virus. The Middle S protein plays an important role in virion budding and mediates contact with the nucleocapsid. The antibody is designed as a neutralizing antibody targeting the antigenic loop (AGL) Type A, which exhibits a distinct disulfide bond pattern that determines recognition by different groups of neutralizing antibodies.", "target_protein": "ELQLVESGGGWVQPGGSQRLSCAASMSWVRQAPGKGLEWVATLYVDSVKGRFTISRDNAKNSLFLQMNNLRVEDTAVYYCWGQGTTVSVSSGRIFRSFYINQDGSEKAAWSGNSGGMDV", "metadata": {"pdb_id": "9u9b", "light_chain_seq": "YELTQPPSVSVSPGQTVSIPCSGDKLGNKNVCWFQHKPGQSPVLVIYEVKYRPSGIPERFSGSNSGNTATLTISGTQAMDEAAYFCQTWDSTTVVFGGGTRLTVL", "cdrh1_seq": "GRIFRSFY", "cdrh2_seq": "INQDGSEK", "cdrh3_seq": "AAWSGNSGGMDV", "cdrl1_seq": "KLGNKN", "cdrl2_seq": "EVK", "cdrl3_seq": "QTWDSTTVV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "9u9b", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "HBC34", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "Middle S protein, Hepatitis B virus", "target_domain": "Antigenic loop (AGL)", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibodies (NAbs) recognize HBsAg; NAb HBC neutralizes HBV"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 6914, 16, 25499, 4857, 12, 20733, 1020, 1010, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 5133, 1920, 5576, 61, 2213, 1927, 7977, 44, 3413, 18, 1920, 5576, 61, 2213, 5705, 1925, 2715, 2770, 1922, 19230, 15909, 1930, 10412, 5217, 1956, 1920, 2797, 28712, 1960, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 14606, 5881, 12, 2260, 1024, 13, 2601, 43, 16, 2154, 9826, 43, 4493, 11830, 5403, 3114, 1988, 13554, 5708, 2007, 2413, 2671, 1927, 12130, 3788, 18, 3], "antigen": ["IPQSLDSWWTSLNFLGYRWMALRRFIIFLFILLLALIFLLVLLDYQGMLPVCPLITSTGPCRTCMTTAQGTSMYPSCCCTKPSDGNCTCIPIPSSWAFGKFLWEWASA", "TIPQSLDSWWTSLNFLYRWMALRRFIIFLFILLLALIFLLVLLDYQGMLPVCPLIPGSSTTSTGPCRTCMTMYPSCCCTKPSDGNCTCIPIPSSWAFGKFLWEWASA"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A human Fab, S309 (IGHV3/IGKV1-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (Omicron variant B.1.1.529). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors including ACE2, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a broadly neutralizing sarbecovirus antibody, the parent of the therapeutic sotrovimab.", "target_protein": "EVQLVESGGGVVQPGGSLRLSCAASMHWVRQAPGKGLEWVAFKYYASVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCWGQGTLVTVSGFTFNSYGIRYDGGNANLKDSRYSGSYYDY", "metadata": {"pdb_id": "7tm0", "light_chain_seq": "VIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKV", "cdrh1_seq": "GFTFNSYG", "cdrh2_seq": "IRYDGGN", "cdrh3_seq": "ANLKDSRYSGSYYDY", "cdrl1_seq": "QDIRFY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYDNLPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9c44", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 7254, 1935, 2830, 6031, 44, 18, 21, 18, 21, 18, 4764, 1026, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 2710, 8298, 1028, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 9851, 12409, 7414, 3533, 16, 1920, 6162, 1927, 1920, 4272, 2577, 1997, 25210, 3368, 1014, 18, 3], "antigen": ["QCVNLQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVIKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKSLLIVNNATNVVIKVCEFQFCNDPFLDHEFRVYSSANNCTFEYVSQPFLFKNLREFVFKNGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQSQSIIAYTMSLGAENSVACSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTICSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDKPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPEL"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A human Fab, 8062 (IGHV1/IGLV3-Lambda), targeting the gp41 helix of Human Immunodeficiency Virus 1. The gp41 helix is part of the envelope protein that mediates viral entry through membrane fusion. This antibody forms a complex with the gp41 helix within the Retroviral envelope protein GP41-like, binding as one of three Fab molecules to a single trimeric N-HR coiled-coil target.", "target_protein": "QLVQSGAEVKKPGSSVKVSCKASFSWVRQAPGQGLEWMGSVYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCWGQGTLVTVSSAGGTFNSYAIIPLFGFVARYFDTYNNYGFAN", "metadata": {"pdb_id": "4khx", "light_chain_seq": "IELTQPPSVSVVPGQTARISCSGDNIPYEYASWYQQKPGQAPVLVIYGDNNRPSGIPERFSGSNSGNTATLTISGTQAEDEADYYCASWDSMTVDGVFGGGTKLTVLGQ", "cdrh1_seq": "GGTFNSYA", "cdrh2_seq": "IIPLFGFV", "cdrh3_seq": "ARYFDTYNNYGFAN", "cdrl1_seq": "NIPYEY", "cdrl2_seq": "GDN", "cdrl3_seq": "ASWDSMTVDGV", "cdrh1_pos": "[23, 30]", "cdrh2_pos": "[48, 55]", "cdrh3_pos": "[94, 107]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 96]", "cdrh3_split": "val", "cdrh3_cluster": "4khx", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "8062", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "gp41 helix, Human Immunodeficiency Virus 1", "target_domain": "Retroviral envelope protein GP41-like", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 3729, 8166, 12, 20733, 7390, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 5133, 1920, 25618, 7864, 1927, 2616, 13141, 3413, 21, 18, 1920, 25618, 7864, 1977, 3131, 1927, 1920, 11262, 2213, 1988, 10412, 4324, 6904, 2596, 3260, 5289, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 25618, 7864, 2651, 1920, 16599, 11262, 2213, 25618, 17, 3189, 16, 2743, 1966, 2340, 1927, 2559, 6914, 4206, 1942, 43, 2957, 29177, 56, 17, 3668, 17524, 17, 9121, 2758, 18, 3], "antigen": ["CCGGIKKEIEAIKKEQEAIKKKIEAIEKELSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARIL"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A human Fab, LAH31 (IGHV1/IGKV2-Kappa), targeting the Hemagglutinin HA2 chain of Influenza A virus. Hemagglutinin binds to sialic acid-containing receptors on the cell surface and mediates fusion of viral and endosomal membranes during viral entry. The antibody is designed to recognize a postfusion-specific epitope with a kinked loop-helix structure that emerges after conformational conversion and is accessible on infected cells, enabling Fc-dependent protection against diverse influenza strains through ADCC-mediated clearance of infected cells.", "target_protein": "VQLEQSGAEVKKPGSSVKVSCKASFSWVRQAPGQGLEWMGRNYAQKFQGRVTFTADKSTATSYMELRSLKSEDTAVYYCWGLGTTVTVSSGGPMFSRSAIIPTVDLKARMGSGSSYYGMDV", "metadata": {"pdb_id": "8ib1", "light_chain_seq": "DIVMTQSPLSLPVIPGEPASISCRSSQSLLQSNGNNYLDWYLQKPGQSPQLLIYLGSNRASGVPDRFSGSGSGTDFTLTISRVEAEDVGVYYCLQARQSSVLTFGGGTKLEIKRT", "cdrh1_seq": "GPMFSRSA", "cdrh2_seq": "IIPTVDLK", "cdrh3_seq": "ARMGSGSSYYGMDV", "cdrl1_seq": "QSLLQSNGNNY", "cdrl2_seq": "LGS", "cdrl3_seq": "LQARQSSVLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 108]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 102]", "cdrh3_split": "val", "cdrh3_cluster": "8ib1", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "LAH31", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Hemagglutinin HA2 chain, Influenza A virus", "target_domain": null, "functional_role": "other", "evidence_quote": "confers protection in an Fc dependent manner via ADCC"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 2616, 6914, 16, 5114, 18649, 1009, 12, 20733, 7390, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 26141, 2118, 1028, 4659, 1927, 7108, 43, 3413, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1930, 10412, 5289, 1927, 4324, 1930, 16514, 5726, 2409, 4324, 6904, 18, 1920, 3533, 1977, 4609, 1942, 9967, 43, 2753, 9049, 17, 2487, 10095, 1956, 43, 30322, 1919, 5881, 17, 7864, 3170, 1988, 22354, 2256, 8523, 7309, 1930, 1977, 10551, 1990, 4014, 2094, 16, 12180, 6437, 17, 3100, 6202, 3316, 6445, 7108, 4046, 2596, 25899, 17, 3434, 7802, 1927, 4014, 2094, 18, 3], "antigen": ["VALENQHTIDLTD"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A human Fab, WCSL 129 (IGHV3/IGLV1-Lambda), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptor ACE2, initiating infection, and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that blocks SARS-CoV-2 virus entry, binding within the Receptor-binding domain (RBD) at an epitope that overlaps the ACE2 interaction site.", "target_protein": "EVQLLESGGGLVQPGGSLRLSCAASMTWVRQAPGKGLEWVSAYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTMVTVSSAGFTFSRFAISGSGGSTAKVGWGAFDI", "metadata": {"pdb_id": "7mzi", "light_chain_seq": "SVLTQPPSASGTPGQSVSISCSGTYSNIGSNPVNWYQQVPGTAPKLLIYANDQRPSGVPDRFSGSKSATSAFLAIGGLQSEDDADYYCSTWDDSLPGPLFGGGTKLTVLGQ", "cdrh1_seq": "GFTFSRFA", "cdrh2_seq": "ISGSGGST", "cdrh3_seq": "AKVGWGAFDI", "cdrl1_seq": "YSNIGSNP", "cdrl2_seq": "AND", "cdrl3_seq": "STWDDSLPGPL", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 105]", "cdrl1_pos": "[24, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "7mzi", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "WCSL 129", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "potent human monoclonal antibodies that block SARS-CoV-2 virus entry"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 2616, 6914, 16, 14888, 1036, 1024, 9367, 12, 20733, 1020, 1010, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 3148, 8298, 1028, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 20466, 17, 6083, 17, 22, 3413, 6904, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 2019, 1925, 10095, 1988, 19853, 1920, 8298, 1028, 2835, 3200, 18, 3], "antigen": ["NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPGS"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab, 38-1-10A (IGHV4/IGKV1-Kappa), targeting the EV71 capsid of Enterovirus A71. The EV71 capsid proteins VP1, VP2, and VP3 form the viral shell and undergo conformational changes upon receptor binding to facilitate viral genome entry into the host cell. The antibody is designed as a neutralizing antibody that prevents receptor binding to the threefold plateau epitope, conferring protection against lethal EV71 infection across multiple genotypes.", "target_protein": "QLQLQESGPGLVKPSETLSLTCTVSWGWIRQPPGKGLEWIGSYYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCWGQGTLVTVSSGGSISSSSYYIYYSGSTAREITMIAWFDP", "metadata": {"pdb_id": "6z3q", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYNYLLTFGGGTKVEI", "cdrh1_seq": "GGSISSSSYY", "cdrh2_seq": "IYYSGST", "cdrh3_seq": "AREITMIAWFDP", "cdrl1_seq": "QGIRND", "cdrl2_seq": "AAS", "cdrl3_seq": "LQDYNYLLT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6z3q", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "38-1-10A", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "EV71 capsid (VP1, VP2, VP3), Enterovirus A71", "target_domain": "threefold plateau", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibodies conferring effective protection against lethal EV71 challenge in vivo"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 3738, 17, 21, 17, 18241, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 2180, 9948, 14681, 1927, 5553, 7414, 27913, 1009, 18, 1920, 2180, 9948, 14681, 2697, 22814, 16, 9314, 1028, 16, 1930, 9314, 1010, 2386, 1920, 4324, 9929, 1930, 4978, 8523, 2840, 4073, 3148, 2743, 1942, 6628, 4324, 3843, 6904, 2460, 1920, 4423, 2024, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 10299, 3148, 2743, 1942, 1920, 23109, 13383, 10095, 16, 21510, 6202, 3316, 10470, 2180, 9948, 2909, 3436, 3137, 7059, 18, 3], "antigen": ["GFPTELKPGTNQFLTTDDGVSAPILPNFHPTPCIHIPGEVRNLLELCQVETILEVNNVPTNATSLMERLRFPVSAQAGKGELCAVFRADPGRDGPWQSTMLGQLCGYYTQWSGSLEVTFMFTGSFMATGKMLIAYTPPGGPLPKDRATAMLGTHVIWDFGLQSSVTLVIPWISNTHYRAHARDGVFDYYTTGLVSIWYQTNYVVPIGAPNTAYIIALAAAQKNFTMKLCKDTSHILQTASIQ", "RVADMIESSIGNSVSRALTQALPAPTGQNTQVSSHRLDTGEVPALQAAEIGASSNTSDESMIETRCVLNSHSTAETTLDSFFSRAGLVGEIDLPLEGTTNPNGYANWDIDITGYAQMRRKVELFTYMRFDAEFTFVACTPTGQVVPQLLQYMFVPPGAPKPESRESLAWQTATNPSVFVKLTDPPAQVSVPFMSPASAYQWFYDGYPTFGEHKQEKDLEYGACPNNMMGTFSVRTVGSSKSKYALVVRIYMRMKHVRAWIPRPMRNQNYLFKANPNYAGDSIKPTGTSRNAITTL", "SDRVAQLTIGNSTITTQEAANIIVGYGEWPSYCSDDDATAVDKPTRPDVSVNRFYTLDTKLWEKSSKGWYWKFPDVLTETGVFGQNAQFHYLYRSGFCIHVQCNASKFHQGALLVAILPEYVIGTVAGGTGTEDSHPPYIQTQPGADGFELQHPYVLDAGIPISQLTVCPHQWINLRTNNCATIIVPYMNTLPFDSALNHCNFGLLVVPISPLDFDQGATPVIPITITLAPMCSEFAGLRQAVTQ"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A murine Fab (IGHV5/IGLV1-Lambda) targeting engineered Hemagglutinin of Influenza A virus with hyperglycosylation modifications. Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and fusion of the viral and endosomal membranes during cell entry. The antibody is designed to recognize a conserved, ordinarily occluded epitope at the HA head interface and confer protection against influenza challenge through Fc-dependent mechanisms. Can you generate its HCDRs?", "target_protein": "VKLVESGEGLVKPGGSLKLSCAASMSWVRQTPEKRLEWVAYYYADTVKGRFTISRDNARNTLYLQMSSLKSEDTAMYYCWDQGTLVTVSGAGFTFSSYDISSGGDYITRVGEYDAWFAY", "metadata": {"pdb_id": "6n5d", "light_chain_seq": "QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFAGLIGGTKNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGQ", "cdrh1_seq": "GFTFSSYD", "cdrh2_seq": "ISSGGDYI", "cdrh3_seq": "TRVGEYDAWFAY", "cdrl1_seq": "TGAVTTSNY", "cdrl2_seq": "GTK", "cdrl3_seq": "ALWYSNHWV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 106]", "cdrl1_pos": "[25, 33]", "cdrl2_pos": "[51, 53]", "cdrl3_pos": "[90, 98]", "cdrh3_split": "val", "cdrh3_cluster": "6n5d", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": null, "functional_role": "other", "evidence_quote": "confer Fc-dependent protection in vivo against lethal influenza challenge"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 7135, 6914, 12, 20733, 1020, 1015, 19, 28961, 7390, 17, 18279, 13, 5133, 11091, 26141, 1927, 7108, 43, 3413, 1956, 11903, 4879, 18801, 6055, 6920, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 5289, 1927, 1920, 4324, 1930, 16514, 5726, 2409, 2024, 6904, 18, 1920, 3533, 1977, 4609, 1942, 9967, 43, 5305, 16, 8873, 29588, 22335, 10095, 2019, 1920, 2118, 4469, 6854, 1930, 7909, 6202, 3316, 7108, 6013, 2596, 6437, 17, 3100, 3531, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["TNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGIHHPSTDQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLAT"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A murine Fab, G2 (IGHV1/IGKV3-Kappa), targeting the Spike glycoprotein of Middle East respiratory syndrome-related coronavirus. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host DPP4 receptor to initiate infection and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that prevents MERS-CoV S protein binding to DPP4 through an indirect mechanism dependent on the trimeric spike conformation, binding within the BetaCoV S1-NTD.", "target_protein": "QVQLQQSGGELVKPGASVKLSCKTSISWLKQKPGQSLEWIAWEYNQKFTGKAQVTVDTSSSTAYMQFSSLTTEDSAIYYCWGQGTSVTVSSAGFTFSSSYIYAGTGGTARGGSSFAMDY", "metadata": {"pdb_id": "6pxh", "light_chain_seq": "QLVLTQSPASLAVSLGQRATISCRASESVDNYGISFMNWFQQKPGQPPKLLIHTASNQGSGVPARFSGSGSGTDFSLNIHPVEDDDTAMYFCQQSEEVPLTFGAGTKLEIKRT", "cdrh1_seq": "GFTFSSSY", "cdrh2_seq": "IYAGTGGT", "cdrh3_seq": "ARGGSSFAMDY", "cdrl1_seq": "ESVDNYGISF", "cdrl2_seq": "TAS", "cdrl3_seq": "QQSEEVPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "6pxh", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "G2", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Middle East respiratory syndrome-related coronavirus", "target_domain": "BetaCoV S1-NTD", "functional_role": "neutralizing", "evidence_quote": "neutralizes MERS-CoV by interfering with binding to host receptor dipeptidyl peptidase-4 (DPP4)"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 7135, 6914, 16, 9616, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 5576, 10319, 5481, 4741, 17, 2712, 5548, 10703, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 16423, 1006, 3148, 1942, 11051, 2909, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 10299, 20197, 17, 6083, 61, 2213, 2743, 1942, 16423, 1006, 2596, 1925, 6354, 2856, 3100, 1990, 1920, 29177, 10429, 7748, 16, 2743, 2651, 1920, 4666, 4879, 1020, 4062, 17, 22078, 18, 3], "antigen": ["YVDVGPDSVKSACIEVDIQQTFFDKTWPRPIDVSKADGIIYPQGRTYSNITITYQGLFPYQGDHGDMYVYSAGHATGTTPQKLFVANYSQDVKQFANGFVVRIGAAANSTGTVIISPSTSATIRKIYPAFMLGSSVGNFSDGKMGRFFNHTLVLLPDGCGTLLRAFYCILEPRSGNHCPAGNSYTSFATYHTPATDCSDGNYNRNASLNSFKEYFNLRNCTFMYTYNITEDEILEWFGITQTAQGVHLFSSRYVDLYGGNMFQFATLPVYDTIKYYSIIPHSIRSIQSDRKAWAAFYVYKLQPLTFLLDFSVDGYIRRAIDCGFNDLSQLHCSY"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A murine Fab, prM13 (IGHV1/IGKV4-Kappa), targeting the prM protein of Dengue virus type 2. The prM protein is the flavivirus premembrane structural protein whose cleavage during virion maturation can be inefficient, leaving partially mature virions with uncleaved prM that retain infectivity. The antibody is designed as a neutralizing antibody that targets partially mature prM-containing virions, binding within the Flavivirus polyprotein propeptide, with the objective of blocking attachment to target cells and preventing infection of prM-positive infectious virions. Please output the HCDRs.", "target_protein": "AAQLQESGPELVKPGASVKISCKASINWVRQSHGKSLEWIGDTYNQKFEGKATLTVDKSSSTAYMELRSLTSDDSAVYYCWGQGTLVTVSAAGYTFTDYFFYPNNRGPARGLWDAWLSY", "metadata": {"pdb_id": "8fe4", "light_chain_seq": "AIVATQSPAIMSASPGEKVTISCSASSSVSYMYWYQQKPGSSPKPWIYRTSNLASGVPTRFSGSGSGTSYSFTISSMEAEDAATYYCQQYHNYPRTFGGGTKAKSARA", "cdrh1_seq": "GYTFTDYF", "cdrh2_seq": "FYPNNRGP", "cdrh3_seq": "ARGLWDAWLSY", "cdrl1_seq": "SSVSY", "cdrl2_seq": "RTS", "cdrl3_seq": "QQYHNYPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "8fe4", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "prM13", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "prM protein, Dengue virus type 2", "target_domain": "Flavivirus polyprotein propeptide", "functional_role": "neutralizing", "evidence_quote": "prM-reactive antibodies neutralized DENV infection in a virion maturation state\u2013dependent manner"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 23043, 3633, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 16, 5133, 1920, 23043, 2213, 1927, 13304, 3413, 2601, 22, 18, 1920, 23043, 2213, 1977, 1920, 26248, 6546, 8591, 4346, 2213, 6098, 6404, 2409, 19230, 7655, 2112, 1998, 20326, 16, 12136, 6426, 6665, 16507, 1956, 6320, 9166, 23043, 1988, 13562, 16217, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 4845, 6426, 6665, 23043, 17, 3165, 16507, 16, 2743, 2651, 1920, 26248, 6240, 5684, 5062, 8253, 16, 1956, 1920, 4470, 1927, 7472, 8576, 1942, 2758, 2094, 1930, 8444, 2909, 1927, 23043, 17, 2843, 7465, 16507, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMADLGELCEDTITYKCPLLRQNEPEDIDCWCNSTSTWVTYGTCT"]} {"modality_type": "antibody", "text": "Output the HCDRs for an antibody that performs this function: A human Fab, DH511.2 (IGHV3/IGKV1-Kappa), targeting the membrane-proximal external region (MPER) of HIV-1 gp41. The gp41 MPER is part of the envelope glycoprotein that mediates fusion of viral and host cell membranes during entry. The antibody is designed as a broadly neutralizing antibody targeting the distal MPER, recognizing a transiently exposed intermediate conformation of gp41 that is induced after CD4-mediated Env activation, binding within the MPER domain.", "target_protein": "QVQLVQSGGGLVKPGGSLTLSCSASMGWVRQAPGKGLEWVGREYGAAVKDRFTISRDDSRNMLYLHMRTLKTEDSGTYYCWGRGTTVIVSSAGFFFDNSWIRRLKDGATGTMDEGTPVTRFLEWGYFYYYMAV", "metadata": {"pdb_id": "5u3k", "light_chain_seq": "DIVMTQSPSSVSASVGDRVTITCRASQNIRDYLNWYQHKPGGSPRLLIYAASTLQTGVPSRFSGSGSGNLFTLTITNLQPEDFATYYCQENYNTIPSLSFGQGTKVDIRRT", "cdrh1_seq": "GFFFDNSW", "cdrh2_seq": "IRRLKDGATG", "cdrh3_seq": "TMDEGTPVTRFLEWGYFYYYMAV", "cdrl1_seq": "QNIRDY", "cdrl2_seq": "AAS", "cdrl3_seq": "QENYNTIPSLS", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 120]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "5u3m", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DH511.2", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "gp41 MPER peptide, Human immunodeficiency virus 1", "target_domain": "MPER; binding to GalCer", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing distal MPER bnAbs...neutralized 206 of 208 viruses (99%)"}}}, "tokenized_instruction": [2, 6647, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 17436, 2052, 2347, 30, 43, 2616, 6914, 16, 6781, 7912, 1009, 18, 22, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 1927, 3525, 17, 21, 25618, 18, 1920, 25618, 5438, 1915, 1977, 3131, 1927, 1920, 11262, 11424, 1988, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 6583, 5438, 1915, 16, 15667, 43, 12145, 4616, 6129, 7748, 1927, 25618, 1988, 1977, 2719, 2256, 4095, 17, 3434, 11118, 2936, 16, 2743, 2651, 1920, 5438, 1915, 3418, 18, 3], "antigen": ["ASLWNWFDITNWLWYIRKK"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A murine Fv, mAb6D8 (IGHV14/IGKV3-Kappa), targeting the Merozoite surface protein 2 of Plasmodium falciparum 3D7. Merozoite surface protein 2 is an intrinsically disordered, membrane-anchored antigen that may play a role in merozoite attachment to the erythrocyte. The antibody is designed to recognize a conserved N-terminal epitope of MSP2, with the objective of understanding how membrane-anchoring and conformational dynamics modulate antibody recognition of disordered antigens in the context of malaria vaccine development.", "target_protein": "QVQLQQSGDELVKPGASVKLSCTVSIHWMKQRPEQGLEWIGRKYAPKFQDKATMTADTSSNTAYLQLSSLASEDAAVYYCWGQGTLVTVSAGFNIKDDFIDPANGYTATYGVAY", "metadata": {"pdb_id": "4qy8", "light_chain_seq": "DIVLTQSPASLAVSLGQRATISCKASQSVDHDGDSYMNWFQQKPGQSPKLLIYAASNLESGIPARFSGSGSGTDFTLNIHPVEEEDAATYYCQQTNEDPYTFGGGTKLEIK", "cdrh1_seq": "GFNIKDDF", "cdrh2_seq": "IDPANGYT", "cdrh3_seq": "ATYGVAY", "cdrl1_seq": "QSVDHDGDSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQTNEDPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 102]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "4r3s", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "mAb6D8", "antibody_format": "Fv", "heavy_subclass": "IGHV14", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Merozoite surface protein 2, Plasmodium falciparum 3D7", "target_domain": null, "functional_role": "other", "evidence_quote": "antibodies generated to conserved N- and C-terminal regions react poorly with native antigen on parasite surface"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 7135, 11417, 16, 7032, 1016, 1007, 1025, 12, 20733, 7390, 1006, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 6902, 26553, 3154, 2213, 22, 1927, 15663, 13098, 5050, 1027, 18, 6902, 26553, 3154, 2213, 22, 1977, 1925, 20061, 13885, 16, 3260, 17, 17199, 4730, 1988, 2278, 3918, 43, 2770, 1922, 6902, 26553, 8576, 1942, 1920, 15469, 18, 1920, 3533, 1977, 4609, 1942, 9967, 43, 5305, 56, 17, 4262, 10095, 1927, 22064, 1028, 16, 1956, 1920, 4470, 1927, 4339, 2307, 3260, 17, 20816, 1930, 8523, 5565, 8480, 3533, 5708, 1927, 13885, 7769, 1922, 1920, 4491, 1927, 7505, 5955, 2740, 18, 3], "antigen": ["NAYNMSIRRSMAES"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A human Fab, P4J15 (IGHV4/IGKV1-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with the host ACE2 receptor, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a broadly neutralizing antibody that mimics the ACE2 contact region, binding within the Receptor-binding domain (RBD), with activity against diverse SARS-CoV-2 variants including XBB and EG lineages.", "target_protein": "IQQWGAGLLKPSETLSLTCAVYWTWIRQSPGMGLEWIGENYNPSLMSRVTMSRDTSKNQISLKLTSVTAADTAVYYCWGQGTLVTDESFSDYFVTHTGSAARDSPLGSIIKRGDY", "metadata": {"pdb_id": "8pq2", "light_chain_seq": "VGDRVTVTCQASQGITNYVNWYQQKPGKAPKLLIYHASHLETGVPSRFSGSGSGTDFTFTISSLQPEDFATYYCQQFDHLPPTFG", "cdrh1_seq": "DESFSDYF", "cdrh2_seq": "VTHTGSA", "cdrh3_seq": "ARDSPLGSIIKRGDY", "cdrl1_seq": "QGITNY", "cdrl2_seq": "HAS", "cdrl3_seq": "QQFDHLPP", "cdrh1_pos": "[22, 29]", "cdrh2_pos": "[47, 53]", "cdrh3_pos": "[92, 106]", "cdrl1_pos": "[12, 17]", "cdrl2_pos": "[35, 37]", "cdrl3_pos": "[74, 81]", "cdrh3_split": "val", "cdrh3_cluster": "8pq2", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "P4J15", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "potent, broad-spectrum neutralizing antibody against all variants including XBB.2.3 and EG.5.1"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 2616, 6914, 16, 9068, 23554, 1015, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 1920, 4423, 8298, 1028, 3148, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1988, 14679, 1920, 8298, 1028, 5217, 3031, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 1956, 2455, 3316, 6445, 20466, 17, 6083, 17, 22, 4936, 2710, 20584, 1014, 1930, 7282, 10439, 18, 3], "antigen": ["CPFHEVFNATTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGSNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVC"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A human Fab (IGHV4/IGKV3-Kappa) targeting a peptide derived from the D1 domain insertion loop of Lymphocyte activation gene 3 protein. LAG-3 is an inhibitory receptor on antigen-activated T cells that delivers inhibitory signals upon binding to ligands such as MHC class II and FGL1, thereby suppressing T-cell activation and antitumor immune responses. The antibody is designed to block LAG-3 engagement with its ligands MHC II and FGL1, reversing LAG-3\u2013mediated T-cell inhibition to restore antitumor immunity, binding within the Ig-like V-type domain. Please provide the HCDR sequences.", "target_protein": "QVQLQQWGAGLLKPSETLSLTCAVYWNWIRQPPGKGLEWIGENSNPSLKSRVTLSLDTSKNQFSLKLRSVTAADTAVYYCWGQGTLVTVSSAGFSDYYINHNGNTAFGYSDYEYNWFDP", "metadata": {"pdb_id": "7um3", "light_chain_seq": "EIVLTQSPATLSLSPGERATLSCRASQSISSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPLTFGQGTNLEIKRT", "cdrh1_seq": "GFSDYY", "cdrh2_seq": "INHNGNT", "cdrh3_seq": "AFGYSDYEYNWFDP", "cdrl1_seq": "QSISSY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQRSNWPLT", "cdrh1_pos": "[25, 30]", "cdrh2_pos": "[48, 54]", "cdrh3_pos": "[93, 106]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7um3", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Lymphocyte activation gene 3 protein, Homo sapiens", "target_domain": "Ig-like V-type", "functional_role": "other", "evidence_quote": "block the interaction of LAG-3 with the ligands MHC II and fibrinogen-like protein-1, and to reverse LAG-3\u2013mediated inhibition of T-cell function"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 2616, 6914, 12, 20733, 1020, 1006, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 43, 4207, 3595, 2037, 1920, 8524, 3418, 7413, 5881, 1927, 10009, 2936, 2359, 23, 2213, 18, 9333, 17, 23, 1977, 1925, 5431, 3148, 1990, 4730, 17, 4128, 62, 2094, 1988, 30070, 5431, 4771, 4073, 2743, 1942, 6908, 2427, 1966, 8709, 2921, 2890, 1930, 13320, 8053, 16, 6113, 13556, 62, 17, 2024, 2936, 1930, 11775, 3743, 3387, 18, 1920, 3533, 1977, 4609, 1942, 3367, 9333, 17, 23, 9577, 1956, 2496, 6908, 8709, 2890, 1930, 13320, 8053, 16, 26526, 9333, 17, 23, 229, 3434, 62, 17, 2024, 3523, 1942, 12900, 11775, 7611, 16, 2743, 2651, 1920, 7021, 17, 3189, 64, 17, 2601, 3418, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["GPHPAAPSSWGP"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A murine Fab, S2A5 (IGHV1/IGKV3-Kappa), targeting the engineered Envelopment polyprotein of Severe fever with thrombocytopenia syndrome virus. The Envelopment polyprotein is a structural component of the virion that shields the hydrophobic fusion loops of glycoprotein C and promotes fusion of membranes with the late endosome after receptor-mediated endocytosis. The antibody is designed as a broadly neutralizing antibody targeting domain I of Gn, capable of inhibiting both viral attachment and fusion steps, with the objective of engaging multiple Gn protomers on the virion surface to achieve potent neutralization across all six SFTSV genotypes.", "target_protein": "EVQLQQSGPELVKPGASVKVSCKASMYWVKQSHGKSLEWIGYSYNQKFKGKATLTVDKSSSTAFMHLNSLTSEDSAVYYCWGQGTSVTVSSGYSFSDDNIDPDNGGTAREDYYGSRAMDY", "metadata": {"pdb_id": "8xk6", "light_chain_seq": "DIVLTQSPASLAVSLGQRATISCKASQSVDYAGDSYMNWYQQKPGQPPKLLIYAASNLESAIPARFSGSGSGTDFTLNIHPVQEEDAATYYCQQSYEDPRTFGGGTKLEIK", "cdrh1_seq": "GYSFSDDN", "cdrh2_seq": "IDPDNGGT", "cdrh3_seq": "AREDYYGSRAMDY", "cdrl1_seq": "QSVDYAGDSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSYEDPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "8xk6", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S2A5", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Envelopment polyprotein, Severe fever with thrombocytopenia syndrome virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "S2A5 provides both pre- and post-exposure protections against SFTSV infection in vivo"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 19470, 1015, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 9840, 2017, 6240, 5684, 1927, 4010, 9087, 1956, 17100, 4741, 3413, 18, 1920, 9840, 2017, 6240, 5684, 1977, 43, 4346, 4594, 1927, 1920, 19230, 1988, 19397, 1036, 1920, 7919, 5289, 11109, 1927, 11424, 45, 1930, 7383, 5289, 1927, 5726, 1956, 1920, 5058, 22321, 2256, 3148, 17, 3434, 11914, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 3418, 51, 1927, 9005, 16, 7131, 1927, 7918, 2321, 4324, 8576, 1930, 5289, 5983, 16, 1956, 1920, 4470, 1927, 15888, 3137, 9005, 23583, 27306, 1990, 1920, 19230, 3154, 1942, 6230, 6828, 14377, 3436, 2136, 3798, 6347, 1973, 1020, 7059, 18, 3], "antigen": ["TGPIICAGPIHSNKSADIPHLLGYSEKICQIDRLIHVSSWLRNHSQFQGYVGQRGGRSQVSYYPAENSYSRWSGLLSPCDADWLGMLVVKKAKGSDMIVPGPSYKGKVFFERPTFDGYVGWGCGSGKSRTESGELCSSDSRTSSGLLPSDRVLWIGDVACQPMTPIPEETFLELKSFSQSEFPDICKIDGIVFNQCEGESLPQPFDVAWMDVGHSHKIIMREHKTKWVQESSSKDFVCYKEGTGPCSESEEKTCKTSGSCRGDMQFCKVAGCEAKCRCSLVHKPGEVVVSYGGMRVRPKCYGFSRMMATLEVS"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human nanobody, N235 (IGHV3/IGKV1-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes during entry. The antibody is designed as a broadly neutralizing antibody targeting a conserved, cryptic epitope in the N-terminal domain (NTD), binding within the BetaCoV S1-NTD. What would the HCDRs be?", "target_protein": "EVQLVESGGGVVQPGGSLRLSCAASMHWVRQAPGKGLEWVAFYYADSVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCWGQGTLVTVSSAGFTFNSYGIRYDGGNKANLKDSRYSGSYYDY", "metadata": {"pdb_id": "8jva", "light_chain_seq": "VIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKVDFKRT", "cdrh1_seq": "GFTFNSYG", "cdrh2_seq": "IRYDGGNK", "cdrh3_seq": "ANLKDSRYSGSYYDY", "cdrl1_seq": "QDIRFY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYDNLPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9c44", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "N235", "antibody_format": "nanobody", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "BetaCoV S1-NTD", "functional_role": "neutralizing", "evidence_quote": "displaying broad neutralization against the SARS-CoV-2 prototype and multiple variants, including the newly emerged Omicron and its sub-variants"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 29773, 2756, 16, 9585, 5798, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 43, 5305, 16, 21565, 10095, 1922, 1920, 56, 17, 4262, 3418, 12, 22078, 13, 16, 2743, 2651, 1920, 4666, 4879, 1020, 4062, 17, 22078, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["QLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISTKRFDNPVLPFNDGVYFASIEKSNIIGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHEFRVYSSANNCTFEYVSQPFLFKNLREFVFKNIDGYFKIYSKHTPIREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTL"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab, 1-87 (IGHV1/IGLV2-Lambda), targeting the engineered prefusion Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting the N-terminal domain (NTD) supersite, a glycan-bordered surface formed by a mobile \u03b2-hairpin and flexible loops at the periphery of the spike.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKVSMHWVRQAPGKGLEWMGGIYAQKFQGRVTMTEDTSTDTAYMELSSLRSEDTAVYYCWGQGTTVTVSGYTLIELSFDPEDAETATGIAVIGPPPSTYYYYGMDV", "metadata": {"pdb_id": "7l2d", "light_chain_seq": "QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTYVFGTGTKVTV", "cdrh1_seq": "GYTLIELS", "cdrh2_seq": "FDPEDAET", "cdrh3_seq": "ATGIAVIGPPPSTYYYYGMDV", "cdrl1_seq": "SSDVGGYNY", "cdrl2_seq": "DVS", "cdrl3_seq": "SSYTSSSTYV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 116]", "cdrl1_pos": "[25, 33]", "cdrl2_pos": "[51, 53]", "cdrl3_pos": "[90, 99]", "cdrh3_split": "val", "cdrh3_cluster": "7l2d", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "1-87", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV2", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "N-terminal domain (NTD)", "functional_role": "neutralizing", "evidence_quote": "potent NTD-directed neutralizing antibodies"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 21, 17, 5783, 12, 20733, 7390, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 11091, 9328, 2670, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 56, 17, 4262, 3418, 12, 22078, 13, 12636, 2394, 16, 43, 15060, 17, 9380, 1919, 3154, 5333, 2007, 43, 8785, 161, 17, 14565, 1930, 9964, 11109, 2019, 1920, 13119, 1927, 1920, 10429, 18, 3], "antigen": ["QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLAAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A murine Fab (IGHV14/IGKV4-Kappa) targeting the Ig-like V-type domain of human Tyrosine-protein phosphatase non-receptor type substrate 1 (SIRP\u03b1). SIRP\u03b1 is a myeloid-specific immune checkpoint receptor that engages the CD47 \"don't eat me\" signal on tumors and normal tissues, mediating negative regulation of phagocytosis and dendritic cell activation. The antibody is designed to disrupt SIRP\u03b1 binding to CD47, thereby unleashing myeloid cell-dependent killing of tumor cells when combined with tumor-opsonizing antibodies.", "target_protein": "EVQLQQSGAELVKPGASVKLSCTASIHWVQQRTEQGLEWIGRKYAPKFQDKATITADTSSNTAYLHLSSLTSEDTAVYYCWGQGTLVTVSAAGFNIKDYYIDPEDGETARWGAY", "metadata": {"pdb_id": "6bit", "light_chain_seq": "IVLTQSPAIMSASPGEKVTLTCASSSVSSSYLYWYQQKPGSSPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSMEAEDAASYFCHQWSSYPRTFGAGTKLELKRA", "cdrh1_seq": "GFNIKDYY", "cdrh2_seq": "IDPEDGET", "cdrh3_seq": "ARWGAY", "cdrl1_seq": "SSVSSSY", "cdrl2_seq": "STS", "cdrl3_seq": "HQWSSYPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 101]", "cdrl1_pos": "[24, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6bit", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV14", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Tyrosine-protein phosphatase non-receptor type substrate 1 (SIRP\u03b1), Homo sapiens", "target_domain": "Ig-like V-type", "functional_role": "other", "evidence_quote": "disrupts SIRP\u03b1 binding to CD47, augments myeloid cell-dependent killing of tumor cells"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 7390, 1006, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1920, 7021, 17, 3189, 64, 17, 2601, 3418, 1927, 2616, 6941, 17, 2213, 8167, 2447, 17, 3148, 2601, 4510, 21, 12, 4520, 1034, 1071, 13, 18, 4520, 1034, 1071, 1977, 43, 9677, 17, 2487, 3743, 11714, 3148, 1988, 11580, 1036, 1920, 29741, 6, 4330, 11, 62, 13619, 2142, 6, 2733, 1990, 3861, 1930, 2791, 3878, 16, 10239, 3136, 3640, 1927, 13715, 1930, 8104, 2024, 2936, 18, 1920, 3533, 1977, 4609, 1942, 12512, 4520, 1034, 1071, 2743, 1942, 29741, 16, 6113, 4774, 18013, 7969, 2029, 9677, 2024, 17, 3100, 11879, 1927, 2798, 2094, 2469, 4252, 1956, 2798, 17, 26303, 3903, 3788, 18, 3], "antigen": ["EELQVIQPDKSVLVAAGETATLRCTATSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRIGNITPADAGTYYCVKFRKGSPDDVEFKSGAGTELSVRA"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A human Fab, 447-52D (IGHV3/IGLV1-Lambda), targeting the V3 loop of gp120 from Human immunodeficiency virus type 1 group M subtype B. The V3 loop mediates attachment of the virus to the host lymphoid cell by binding to the primary receptor CD4, inducing structural rearrangement that creates a high-affinity binding site for chemokine coreceptors. The antibody is designed as a neutralizing antibody capable of recognizing diverse V3 sequences while maintaining specificity for the conserved GPxR core epitope, binding within the V3 domain.", "target_protein": "EVQLVESGGGLVKPGGSLRLTCVASLNWVRQAPGKGLEWVGRDYAASVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYSCWGKGTTVTVSSAGFTFSDVWIKSRTDGGTTTTDGFIMIRGVSEDYYYYYMDV", "metadata": {"pdb_id": "1q1j", "light_chain_seq": "QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVLWYQQFPGTAPKLLIYGNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYFCATWDSGLSADWVFGGGTKLTVLSQ", "cdrh1_seq": "GFTFSDVW", "cdrh2_seq": "IKSRTDGGTT", "cdrh3_seq": "TTDGFIMIRGVSEDYYYYYMDV", "cdrl1_seq": "SSNIGNNY", "cdrl2_seq": "GNN", "cdrl3_seq": "ATWDSGLSADWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 119]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 100]", "cdrh3_split": "val", "cdrh3_cluster": "4m1d", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "447-52D", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "gp120 V3 peptide, Human immunodeficiency virus type 1 group M subtype B", "target_domain": "V3", "functional_role": "neutralizing", "evidence_quote": "neutralizes both X4 and R5 primary isolates, one of the most effective anti-V3 antibodies"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 2616, 6914, 16, 29146, 17, 4764, 1007, 12, 20733, 1020, 1010, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 14307, 5881, 1927, 16102, 2037, 2616, 13141, 3413, 2601, 21, 2210, 55, 8856, 44, 18, 1920, 14307, 5881, 10412, 8576, 1927, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1988, 15628, 43, 2149, 17, 5173, 2743, 3200, 1958, 11673, 30435, 3448, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 7131, 1927, 15667, 6445, 14307, 3709, 2679, 8231, 4896, 1958, 1920, 5305, 23151, 1005, 4728, 10095, 16, 2743, 2651, 1920, 14307, 3418, 18, 3], "antigen": ["KRIHIGPGRA"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A murine Fab (IGHV5/IGKV1-Kappa) targeting the trimeric Membrane protein TRIC of Sulfolobus solfataricus. This antibody is intended as a structural tool to facilitate crystallization and structure determination of the prokaryotic TRIC channel, enabling high-resolution structural characterization of this ion channel superfamily. Please generate the HCDRs for this antibody.", "target_protein": "VKLVESGGGLVKPGGSLKLSCAASMSWVRQTPEKRLEWVAYYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCWGQGTLVTVSAAGFGFTIYDMSSGRGNTTRGAFYYGYGFAY", "metadata": {"pdb_id": "5h35", "light_chain_seq": "DIVMTQTPLSLPVSLGDQASISCRSSQFIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPWTFGGGTKLEIKRA", "cdrh1_seq": "GFGFTIYD", "cdrh2_seq": "MSSGRGNT", "cdrh3_seq": "TRGAFYYGYGFAY", "cdrl1_seq": "QFIVHSNGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQGSHVPWT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 107]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "5h35", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Membrane protein TRIC, Sulfolobus solfataricus", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "Further crystallization of SsTRIC in complex with the Fab fragment of a monoclonal antibody"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 1020, 1015, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 29177, 3260, 2213, 12258, 1927, 5141, 26356, 26835, 2638, 6016, 3857, 3133, 1957, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 6628, 15416, 1930, 3170, 7063, 1927, 1920, 21545, 12258, 4999, 16, 12180, 2149, 17, 4885, 4346, 7285, 1927, 2052, 4755, 4999, 13975, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["MYMILELLNIIGIIAFTISGSLKGTNKGLDIFGVVTLGVITSYAGGIIADILLGIYPPQILKELNYLLLSVGISIFVFYFYKWLQTNPIKMIIAISDAVGLSTFATLGASLAYSYGLNPISVGLIAAIVGTGGGVIRDVLVNEIPMVLTKEIYATAALLSGFIYYFTTPYLHHDSLFVAFLGSFLLRILSIKYNF"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A murine Fab (IGHV1/IGKV16-Kappa) targeting the cytochrome c-dependent nitric oxide reductase (cNOR) complex, comprising Nitric oxide reductase subunits B and C from Pseudomonas aeruginosa. Nitric oxide reductase subunit B is the catalytic subunit of the anaerobic respiratory chain that transforms nitric oxide to nitrous oxide via reductive coupling at a heme/non-heme Fe center and shows proton pump activity across the membrane. This antibody is intended as a structural tool to facilitate crystallographic characterization of the reduced and ligand-bound forms of cNOR. Please generate its HCDRs.", "target_protein": "EVQLQQSGTVLARPGASVKMSCKASMHWVKQRPGQGLEWIGASYNQKFKGKAKLTAVTSASTAYMELSSLTNEDSAVYYCWGQGTTVTVSSAGYSFTSYWVYPGNSDTSRSSLDGYYVKNWCFDV", "metadata": {"pdb_id": "3wfb", "light_chain_seq": "DIQMTQSPPYLAASPGETITINCRASKSIRKYLAWYQEKPGKTNKLLIYSGSTLQFGIPSRFSGSGSGTEFTLTISSLEPEDFAMYYCQQHNEYPLTFGAGTKLELKRA", "cdrh1_seq": "GYSFTSYW", "cdrh2_seq": "VYPGNSDT", "cdrh3_seq": "SRSSLDGYYVKNWCFDV", "cdrl1_seq": "KSIRKY", "cdrl2_seq": "SGS", "cdrl3_seq": "QQHNEYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3o0r", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV16", "is_engineered": false, "target_antigen": "Nitric oxide reductase subunits B and C, Pseudomonas aeruginosa", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "antibody fragment used in crystallographic structure determination"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 1016, 17, 12093, 13, 5133, 1920, 9387, 45, 17, 3100, 10233, 7491, 11386, 12, 5940, 1924, 13, 2796, 16, 10351, 10233, 7491, 11386, 6991, 44, 1930, 45, 2037, 13461, 10830, 18, 10233, 7491, 11386, 5903, 44, 1977, 1920, 6804, 5903, 1927, 1920, 12554, 5481, 4659, 1988, 29584, 10233, 7491, 1942, 8686, 1957, 7491, 3454, 23335, 7590, 2019, 43, 10954, 19, 2447, 17, 10954, 2650, 4102, 1930, 3661, 8433, 8912, 2455, 3436, 1920, 3260, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 6628, 17832, 7285, 1927, 1920, 3028, 1930, 5207, 17, 4124, 4952, 1927, 5940, 1924, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["FASQAVAKPYFVFALILFVGQILFGLIMGLQYVVGDFLFPAIPFNVARMVHTNLLIVWLLFGFMGAAYYLVPEESDCELYSPKLAWILFWVFAAAGVLTILGYLLVPYAGLARLTGNELWPTMGREFLEQPTISKAGIVIVALGFLFNVGMTVLRGRKTAISMVLMTGLIGLALLFLFSFYNPENLTRDKFYWWWVVHLWVEGVWELIMGAILAFVLVKITGVDREVIEKWLYVIIAMALISGIIGTGHHYFWIGVPGYWLWLGSVFSALEPLPFFAMVLFAFNTINRRRRDYPNRAVALWAMGTTVMAFLGAGVWGFMHTLAPVNYYTHGTQLTAAHGHMAFYGAYAMIVMTIISYAMPRLRGIGEAMDNRSQVLEMWGFWLMTVAMVFITLFLSAAGVLQVWLQRMPADGAAMTFMATQDQLAIFYWLREGAGVVFLIGLVAYLLSF", "FTKGMARNIYFGGSVFFILLFLALTYHTEKTLPERTNEAAMSAAVVRGKLVWEQNNCVGCHTLLGEGAYFAPELGNVVGRRGGEEGFNTFLQAWMKIQPLNVPGRRAMPQFHLSEGQVDDLAEFLKWSSKIDTNQWPPNKEG"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A murine Fab, ACT-1 (IGHV1/IGKV1-Kappa), targeting the integrin alpha-4/beta-7 heterodimer of Homo sapiens. Integrin alpha-4/beta-7 is a lymphocyte homing receptor that mediates lymphocyte migration and homing to gut-associated lymphoid tissue through interaction with mucosal adhesion molecules including MAdCAM-1, VCAM-1, and fibronectin. The antibody is designed to bind the specificity-determining loop (SDL) of the beta-7 subunit at the alpha-4/beta-7 interface, functioning as a structural tool to stabilize and characterize the integrin headpiece conformation in its closed state. Please output the HCDRs.", "target_protein": "QVQLQQPGAELVKPGTSVKLSCKGYMHWVKQRPGQGLEWIGENYNQKFKGKATLTVDISSSTAYMQLSSLTSEDSAVYYCWGQGTSVTVSSAGYTFTSYWIDPSESNTARGGYDGWDYAIDY", "metadata": {"pdb_id": "3v4v", "light_chain_seq": "DVVVTQTPLSLPVSFGDQVSISCRSSQSLAKSYGNTYLSWYLHKPGQSPQLLIYGISNRFSGVPDRFSGSGSGTDFTLKISTIKPEDLGMYYCLQGTHQPYTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTSYW", "cdrh2_seq": "IDPSESNT", "cdrh3_seq": "ARGGYDGWDYAIDY", "cdrl1_seq": "QSLAKSYGNTY", "cdrl2_seq": "GIS", "cdrl3_seq": "LQGTHQPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "3v4p", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ACT-1", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Integrin alpha-4/beta-7, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "ACT-1 recognizes the specificity-determining loop (SDL) of integrin beta-7"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 4033, 17, 21, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 8920, 4595, 17, 24, 19, 4666, 17, 27, 15672, 1927, 16350, 27974, 18, 8920, 4595, 17, 24, 19, 4666, 17, 27, 1977, 43, 10009, 20621, 3148, 1988, 10412, 10009, 5049, 1930, 20621, 1942, 7660, 17, 2458, 11751, 2960, 2596, 2835, 1956, 9565, 6141, 4206, 2710, 9133, 15024, 17, 21, 16, 19942, 17, 21, 16, 1930, 12848, 18, 1920, 3533, 1977, 4609, 1942, 4566, 1920, 4896, 17, 7426, 5881, 12, 4035, 1024, 13, 1927, 1920, 4666, 17, 27, 5903, 2019, 1920, 4595, 17, 24, 19, 4666, 17, 27, 6854, 16, 7295, 1966, 43, 4346, 5229, 1942, 13448, 1930, 8063, 1920, 8920, 4469, 10984, 12761, 7748, 1922, 2496, 8047, 3360, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["RGQQEVLQDQPLSQGARGEGATQLAPQRVRVTLRPGEPQQLQVRFLRAEGYPVDLYYLMDLSYSMKDDLERVRQLGHALLVRLQEVTHSVRIGFGSFVDKTVLPFVSTVPSKLRHPCPTRLERCQSPFSFHHVLSLTGDAQAFEREVGRQSVSGNLDSPEGGFDAILQAALCQEQIGWRNVSRLLVFTSDDTFHTAGDGKLGGIFMPSDGHCHLDSNGLYSRSTEFDYPSVGQVAQALSAANIQPIFAVTSAALPVYQELSKLIPKSAVGELSEDSSNVVQLIMDAYNSLSSTVTLEHSSLPPGVHISYESQCEGPEKREGKAEDRGQCNHVRINQTVTFWVSLQATHCLPEPHLLRLRALGFSEELIVELHTLC", "YNVDTESALLYQGPHNTLFGYSVVLHSHGANRWLLVGAPTANWLANASVINPGAIYRCRIGKNPGQTCEQLQLGSPNGEPCGKTCLEERDNQWLGVTLSRQPGENGSIVTCGHRWKNIFYIKNENKLPTGGCYGVPPDLRTELSKRIAPCYQDYVKKFGENFASCQAGISSFYTKDLIVMGAPGSSYWTGSLFVYNITTNKYKAFLDKQNQVKFGSYLGYSVGAGHFRSQHTTEVVGGAPQHEQIGKAYIFSIDEKELNILHEMKGKKLGSYFGASVCAVDLNADGFSDLLVGAPMQSTIREEGRVFVYINSGSGAVMNAMETNLVGSDKYAARFGESIVNLGDIDNDGFEDVAIGAPQEDDLQGAIYIYNGRADGISSTFSQRIEGLQISKSLSMFGQSISGQIDADNNGYVDVAVGAFRSDSAVLLRTRPVVIVDASLSHPESVNRTKFDCVENGWPSVCIDLTLCFSYKGKEVPGYIVLFYNMSLDVNRKAESPPRFYFSSNGTSDVITGSIQVSSREANCRTHQAFMRKDVRDILTPIQIEAAYHLGPHSTEEFPPLQPILQQKKEKDIMKKTINFAR"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A murine Fab (IGHV1/IGKV16-Kappa) targeting the heteromeric nitric oxide reductase complex composed of subunit B and subunit C from Pseudomonas aeruginosa PAO1. Nitric oxide reductase subunit B is the catalytic subunit of the enzyme complex that transforms nitric oxide to dinitrogen as part of the anaerobic respiratory chain (denitrification), while subunit C is a component of the same anaerobic respiratory chain. This antibody forms a complex with the nitric oxide reductase enzyme complex. Please provide the HCDR sequences.", "target_protein": "EVQLQQSGTVLARPGASVKMSCKASMHWVKQRPGQGLEWIGASYNQKFKGKAKLTAVTSASTAYMELSSLTNEDSAVYYCWGQGTTVTVSSAGYSFTSYWVYPGNSDTSRSSLDGYYVKNWCFDV", "metadata": {"pdb_id": "5gux", "light_chain_seq": "DIQMTQSPPYLAASPGETITINCRASKSIRKYLAWYQEKPGKTNKLLIYSGSTLQFGIPSRFSGSGSGTEFTLTISSLEPEDFAMYYCQQHNEYPLTFGAGTKLELKRA", "cdrh1_seq": "GYSFTSYW", "cdrh2_seq": "VYPGNSDT", "cdrh3_seq": "SRSSLDGYYVKNWCFDV", "cdrl1_seq": "KSIRKY", "cdrl2_seq": "SGS", "cdrl3_seq": "QQHNEYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3o0r", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV16", "is_engineered": false, "target_antigen": "Nitric oxide reductase subunit B and subunit C, Pseudomonas aeruginosa PAO1", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 1016, 17, 12093, 13, 5133, 1920, 19732, 9213, 1935, 10233, 7491, 11386, 2796, 7179, 1927, 5903, 44, 1930, 5903, 45, 2037, 13461, 10830, 29880, 18, 10233, 7491, 11386, 5903, 44, 1977, 1920, 6804, 5903, 1927, 1920, 4113, 2796, 1988, 29584, 10233, 7491, 1942, 11687, 4775, 1966, 3131, 1927, 1920, 12554, 5481, 4659, 12, 26319, 3123, 13, 16, 2679, 5903, 45, 1977, 43, 4594, 1927, 1920, 2841, 12554, 5481, 4659, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10233, 7491, 11386, 4113, 2796, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["FASQAVAKPYFVFALILFVGQILFGLIMGLQYVVGDFLFPAIPFNVARMVHTNLLIVWLLFGFMGAAYYLVPEESDCELYSPKLAWILFWVFAAAGVLTILGYLLVPYAGLARLTGNELWPTMGREFLEQPTISKAGIVIVALGFLFNVGMTVLRGRKTAISMVLMTGLIGLALLFLFSFYNPENLTRDKFYWWWVVHLWVEGVWELIMGAILAFVLVKITGVDREVIEKWLYVIIAMALISGIIGTGHHYFWIGVPGYWLWLGSVFSALEPLPFFAMVLFAFNTINRRRRDYPNRAVALWAMGTTVMAFLGAGVWGFMHTLAPVNYYTHGTQLTAAHGHMAFYGAYAMIVMTIISYAMPRLRGIGEAMDNRSQVLEMWGFWLMTVAMVFITLFLSAAGVLQVWLQRMPADGAAMTFMATQDQLAIFYWLREGAGVVFLIGLVAYLLSF", "FTKGMARNIYFGGSVFFILLFLALTYHTEKTLPERTNEAAMSAAVVRGKLVWEQNNCVGCHTLLGEGAYFAPELGNVVGRRGGEEGFNTFLQAWMKIQPLNVPGRRAMPQFHLSEGQVDDLAEFLKWSSKIDTNQWPPNKEG"]} {"modality_type": "antibody", "text": "A human Fab (IGHV3/IGKV1-Kappa) targeting a linear epitope (residues 139-148) within the Large envelope protein of Hepatitis B virus. The Large envelope protein in its external conformation attaches the virus to cell receptors to initiate infection and mediates fusion between virion and endosomal membranes. The antibody is designed as a broadly neutralizing antibody targeting a non-overlapping epitope on HBsAg, part of a complementary antibody combination to suppress escape mutations. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "QVQLVESGGGVAQPGRSLRLSCAASMHWVRQAPGKGLEWVAGYYTDSVKGRFTISRDNSRSTLYLDINSLRAEDTAVYYCWGLGTLVTVSSAGFSFSRHGIWFDGTNDAREDPHLLIATLDL", "metadata": {"pdb_id": "6vjt", "light_chain_seq": "DIQVTQSPSSLSAFVGDRVTITCRASQGLTSFINWYQQKPGRAPKLLISSASSLQRGVPSRFTASGSGTHFTLTISSLQPEDFATYYCQQSYGTPALAFGGGTKVDIKRT", "cdrh1_seq": "GFSFSRHG", "cdrh2_seq": "IWFDGTND", "cdrh3_seq": "AREDPHLLIATLDL", "cdrl1_seq": "QGLTSF", "cdrl2_seq": "SAS", "cdrl3_seq": "QQSYGTPALA", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "6vjt", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Large envelope protein (antigenic region 139-148), Hepatitis B virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibodies (bNAbs) that targeted 3 non-overlapping epitopes on the HBV S antigen"}}}, "tokenized_instruction": [2, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 43, 4258, 10095, 12, 4248, 13316, 17, 13623, 13, 2651, 1920, 3103, 11262, 2213, 1927, 7977, 44, 3413, 18, 1920, 3103, 11262, 2213, 1922, 2496, 5771, 7748, 5823, 1918, 1920, 3413, 1942, 2024, 4086, 1942, 11051, 2909, 1930, 10412, 5289, 2192, 19230, 1930, 16514, 5726, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 43, 2447, 17, 8984, 10095, 1990, 17596, 16, 3131, 1927, 43, 8862, 3533, 3921, 1942, 4400, 11781, 3527, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["STKPSDGNST"]} {"modality_type": "antibody", "text": "A human Fab, ADI-15878 (IGHV3/IGKV1-Kappa), targeting the engineered Envelope glycoprotein of Bundibugyo ebolavirus. The Envelope glycoprotein is a class I viral fusion protein that mediates fusion of viral and target cell membranes during entry and is responsible for penetration of the virus into the cell cytoplasm. The antibody is designed as a pan-ebolavirus neutralizing antibody targeting the internal fusion loop and HR1 region of the glycoprotein. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "VQLVQSGVTLVQPGGSLRVSCAASMSWVRQAPGKGLEWVSAYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGALVTVSGFTFSSYAISGLGGSTAKDHRVWAAGYHFDY", "metadata": {"pdb_id": "6dzm", "light_chain_seq": "DIVLTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGEAPKLLISDASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYYSSPTFGGGTKVEIK", "cdrh1_seq": "GFTFSSYA", "cdrh2_seq": "ISGLGGST", "cdrh3_seq": "AKDHRVWAAGYHFDY", "cdrl1_seq": "QSISSW", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYYSSPT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6dzm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ADI-15878", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Envelope glycoprotein, Bundibugyo ebolavirus", "target_domain": "Internal fusion loop and HR1", "functional_role": "neutralizing", "evidence_quote": "potent human survivor-derived antibody ADI-15878, which has full pan-ebolavirus activity and has shown protection in three stringent animal models"}}}, "tokenized_instruction": [2, 43, 2616, 6914, 16, 2041, 1033, 17, 14340, 7950, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 11262, 11424, 1927, 10051, 2023, 2215, 25749, 24497, 11074, 18, 1920, 11262, 11424, 1977, 43, 2921, 51, 4324, 5289, 2213, 1988, 10412, 5289, 1927, 4324, 1930, 2758, 2024, 5726, 2409, 6904, 1930, 1977, 5061, 1958, 12006, 1927, 1920, 3413, 2460, 1920, 2024, 5239, 18, 1920, 3533, 1977, 4609, 1966, 43, 3797, 17, 24497, 11074, 12130, 3533, 5133, 1920, 4495, 5289, 5881, 1930, 3668, 1009, 3031, 1927, 1920, 11424, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["CNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYTEGIMHNQNGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQ", "IPLGVVHNNTLQVSDIDKLVCRDKLSSTSQLKSVGLNLEGNGVATDVPTATKRWGFRAGVPPKVVNYEAGEWAENCYNLDIKKADGSECLPEAPEGVRGFPRCRYVHKVSGTGPCPEGYAFHKEGAFFLYDRLASTIIYRSTTFSEGVVAFLILPETKKDFTVTLNYVADNFGTNMTNFLFQVDHLTYVQLEPRFTPQFLVQLNETIYTNGRLIWKVNPWAFWE"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A murine Fab (IGHV5/IGKV4-Kappa) targeting a fusion construct of the Type-2 angiotensin II receptor with soluble cytochrome b562 (N- to C-terminus). The Type-2 angiotensin II receptor is a G-protein-coupled receptor that signals via non-canonical G protein- and beta-arrestin independent pathways and cooperates with MTUS1 to inhibit ERK2 activation and cell proliferation. The antibody is designed as a structural tool to stabilize the extended binding domain of the receptor, functioning as a positive allosteric modulator to enable structural characterization of the receptor-ligand complex. Please output the HCDRs.", "target_protein": "DVQLVESGGGLVQPGGSRKLSCAASMHWVRQAPEKGLEWVAYYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTAMYFCWGQGTLVTVSAAGFTFSGFGISSGSSLIATSLYYGTPWFAY", "metadata": {"pdb_id": "5xjm", "light_chain_seq": "DIVLTQSPAIMSASPGEKVTMTCSASSSVTYMYWYQQKPGSSPRLLIYDTSNLASGVPVRFSGSGSGTSYSLTISRMEAEDAATFYCQQWSSYPLTFGAGTKLELKRA", "cdrh1_seq": "GFTFSGFG", "cdrh2_seq": "ISSGSSLI", "cdrh3_seq": "ATSLYYGTPWFAY", "cdrl1_seq": "SSVTY", "cdrl2_seq": "DTS", "cdrl3_seq": "QQWSSYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "5xjm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Type-2 angiotensin II receptor fused to soluble cytochrome b562, Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "antibody fragment to stabilize the extended binding domain that functions as a positive allosteric modulator"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 1020, 1015, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 43, 5289, 6377, 1927, 1920, 2601, 17, 22, 10814, 2890, 3148, 1956, 6622, 9387, 24365, 8166, 12, 56, 17, 1942, 45, 17, 7822, 13, 18, 1920, 2601, 17, 22, 10814, 2890, 3148, 1977, 43, 49, 17, 2213, 17, 6416, 3148, 1988, 4771, 3454, 2447, 17, 9452, 49, 2213, 17, 1930, 4666, 17, 16639, 3484, 3873, 1930, 23230, 1036, 1956, 4638, 1957, 1009, 1942, 2875, 23979, 2936, 1930, 2024, 4031, 18, 1920, 3533, 1977, 4609, 1966, 43, 4346, 5229, 1942, 13448, 1920, 6091, 2743, 3418, 1927, 1920, 3148, 16, 7295, 1966, 43, 2843, 14772, 18521, 1942, 8675, 4346, 7285, 1927, 1920, 3148, 17, 5207, 2796, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["CSQKPSDKHLDAIPILYYIIFVIGFLVNIVVVTLFCCQKGPKKVSSIYIFNLAVADLLLLATLPLWATYYSYRYDWLFGPVMCKVFGSFLTLNMFASIFFITCMSVDRYQSVIYPFLSQRRNPWQASYIVPLVWCMACLSSLPTFYFRDVRTIEYLGVNACIMAFPPEKYAQWSAGIALMKNILGFIIPLIFIATCYFGIRKHLLKTNADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLKNRITRDQVLKMAAAVVLAFIICWLPFHVLTFLDALAWMGVINSCEVIAVIDLALPFAILLGFTNSCVNPFLYCF"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A human Fab, D4-30 (IGKV2-Kappa), targeting the Iron-regulated surface determinant protein B of Staphylococcus aureus. Iron-regulated surface determinant protein B is a cell wall-anchored surface receptor that extracts heme from oxidized metHb to enable growth on hemoglobin as a sole iron source and promotes resistance to hydrogen peroxide and killing by neutrophils. The antibody is designed to block hemoglobin and heme binding to IsdB, binding within the NEAT 2 domain.", "target_protein": "QVQLVQSGSEVKKPGSSVTLSCKASYSWVRQAPGQRLEWIGGKSAPHLQDRLTITANKATRTAYMELTSLTSDDSGVYYCWGQGTLVTVSSAGDTFNTHTIMPIFAASARDGRGALQY", "metadata": {"pdb_id": "5d1x", "light_chain_seq": "DIVMTQSPLSLPVTLGQPASISCSSAQSLVHSDGDSYLTWFHQRPGQSPRRLIYKVSIRDAGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQATHWPYTFGQGTKLEIKRT", "cdrh1_seq": "GDTFNTHT", "cdrh2_seq": "IMPIFAAS", "cdrh3_seq": "ARDGRGALQY", "cdrl1_seq": "QSLVHSDGDSY", "cdrl2_seq": "KVS", "cdrl3_seq": "MQATHWPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 105]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "5d1x", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "D4-30", "antibody_format": "Fab", "heavy_subclass": "unknown", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Iron-regulated surface determinant protein B, Staphylococcus aureus", "target_domain": "NEAT 2", "functional_role": "other", "evidence_quote": "neutralizing antibodies that block haemoglobin binding to IsdB"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 16603, 17, 2627, 12, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 5680, 17, 4335, 3154, 12483, 2213, 44, 1927, 13452, 8849, 18, 5680, 17, 4335, 3154, 12483, 2213, 44, 1977, 43, 2024, 4821, 17, 17199, 3154, 3148, 1988, 6391, 10954, 2037, 11339, 2295, 1014, 1942, 8675, 2905, 1990, 9652, 1966, 43, 12168, 5680, 4585, 1930, 7383, 3554, 1942, 6201, 12316, 1930, 11879, 2007, 8508, 18, 1920, 3533, 1977, 4609, 1942, 3367, 9652, 1930, 10954, 2743, 1942, 1977, 12695, 16, 2743, 2651, 1920, 26283, 22, 3418, 18, 3], "antigen": ["KMTDLQDTKYVVYESVENNESMMDTFVKHPIKTGMLNGKKYMVMETTNDDYWKDFMVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAFT"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A human Fab (IGHV1/IGKV10-Kappa) targeting the T-cell surface glycoprotein CD3 epsilon chain. CD3 epsilon is part of the TCR-CD3 complex on T-lymphocyte cell surfaces and plays an essential role in adaptive immune response by transmitting TCR-mediated signals across the cell membrane through immunoreceptor tyrosine-based activation motifs. This antibody is intended as a structural tool to stabilize and aid cryo-EM structural analysis of the fully assembled gamma-delta TCR-CD3 complex.", "target_protein": "EVQLQQSGPELVKPGASMKISCKASMNWVKQSHGKNLEWMGLTYNQKFKDKATLTVDKSSSTAYMELLSLTSEDSAVYYCWGQGTTLTVGYSFTGYTINPYKGVSARSGYYGDSDWYFDV", "metadata": {"pdb_id": "9cia", "light_chain_seq": "DIQMTQTTSSLSASLGDRVTISCRASQDIRNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSKFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFAGGTKL", "cdrh1_seq": "GYSFTGYT", "cdrh2_seq": "INPYKGVS", "cdrh3_seq": "ARSGYYGDSDWYFDV", "cdrl1_seq": "QDIRNY", "cdrl2_seq": "YTS", "cdrl3_seq": "QQGNTLPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "1xiw", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV10", "is_engineered": false, "target_antigen": "T-cell surface glycoprotein CD3 epsilon chain, Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "Fab fragments of the well-studied CD3\u03b5-specific antibody UCHT1 to aid high-resolution structural analysis"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 1008, 17, 12093, 13, 5133, 1920, 62, 17, 2024, 3154, 11424, 9016, 22206, 4659, 18, 9016, 22206, 1977, 3131, 1927, 1920, 8367, 17, 9016, 2796, 1990, 62, 17, 10009, 2024, 7553, 1930, 5705, 1925, 4415, 2770, 1922, 7617, 3743, 2644, 2007, 27622, 8367, 17, 3434, 4771, 3436, 1920, 2024, 3260, 2596, 8613, 3342, 1924, 6941, 17, 2454, 2936, 8277, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 1930, 8379, 15822, 17, 2391, 4346, 2333, 1927, 1920, 5437, 10151, 7034, 17, 9649, 8367, 17, 9016, 2796, 18, 3], "antigen": ["QTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCENCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNR"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab (IGHV1/IGKV3-Kappa) targeting the engineered Spike protein S1 of Severe acute respiratory syndrome coronavirus 2, one of three antibodies (CB6 mutant, S309, and S304) in a complex with the XBB.1.5 RBD. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors including ACE2, TFRC, GRM2, NRP1/NRP2, ASGR1, and integrin, and mediates fusion of viral and cellular membranes as a class I viral fusion protein. This antibody forms a complex with the Spike protein S1 within the Receptor-binding domain (RBD). Please output the HCDRs.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "8wpw", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike protein S1, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 11091, 10429, 2213, 4062, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 16, 2340, 1927, 2559, 3788, 12, 5529, 1016, 3606, 16, 6080, 13192, 16, 1930, 6080, 14743, 13, 1922, 43, 2796, 1956, 1920, 20584, 1014, 18, 21, 18, 25, 25780, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 2710, 8298, 1028, 16, 26817, 1030, 16, 2398, 8224, 16, 5214, 5113, 19, 5214, 5991, 16, 1966, 2299, 1009, 16, 1930, 8920, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 2213, 4062, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["TNLCPFHEVFNATTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGP"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, BG7-15 (IGHV1/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes during entry. The antibody is designed as a neutralizing antibody that retains potent activity against circulating SARS-CoV-2 variants, recognizing an epitope on the RBD.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKLQGRVTMTTDTSTNTAYMELRSLRSDDTAIYYCWGQGTLVTVGYTFTSYAVSAYNGNTAIPYSSVTFDC", "metadata": {"pdb_id": "7m6g", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQSVSGTFLAWYQQKPGQAPRLLISGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSRPTFGQGTKLEI", "cdrh1_seq": "GYTFTSYA", "cdrh2_seq": "VSAYNGNT", "cdrh3_seq": "AIPYSSVTFDC", "cdrl1_seq": "QSVSGTF", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYGSSRPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "7m6g", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "BG7-15", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody that retains potent neutralizing activity against SARS-CoV-2 variants B.1.1.7 and B.1.351"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 14415, 1027, 17, 2461, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 21645, 6828, 2455, 3316, 7396, 20466, 17, 6083, 17, 22, 4936, 16, 15667, 1925, 10095, 1990, 1920, 25780, 18, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHDNPVLPFNDGVYFASTNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFFRVYSSANNCTFEYVSQPFLKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRNLKPFERDISTENCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICAVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human Fab, RBD-chAb-45 (IGHV1/IGKV6-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors (primarily ACE2) to initiate infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting the receptor-binding domain. Generate the corresponding HCDRs.", "target_protein": "EVQLQQSGPELVKPGASVKISCKTSIYWVKQSLGKSLEWIGGTYKQFFKGKATLTVDKSSSTAYMELRSLTSEDSAVYYCWGQGTSVTVSSGYTFTEYTNNPNNDDTARDGYPYYYALDF", "metadata": {"pdb_id": "7ej5", "light_chain_seq": "DIVMTQSQKFMSTSVGDRVSVTCKSSQNVGTNVAWYQQKPGQSPKALIYSASYRYSGVPDHFTGSGSGTDFTLTISNVQSADLAEYFCQQYNNYPWTFGGGTKLEIKRT", "cdrh1_seq": "GYTFTEYT", "cdrh2_seq": "NNPNNDDT", "cdrh3_seq": "ARDGYPYYYALDF", "cdrl1_seq": "QNVGTN", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYNNYPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7w9e", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "RBD-chAb-45", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 6914, 16, 25780, 17, 13297, 1014, 17, 3607, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 12, 5985, 8298, 1028, 13, 1942, 11051, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 3148, 17, 2743, 3418, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVVYSSANNCTFEYVSQFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A murine single-chain Fv (scFv), UCHT1 (IGHV1/IGKV10-Kappa), targeting the CD3 epsilon/delta heterodimer of the human T-cell surface glycoprotein CD3 complex. The CD3 epsilon and delta chains are part of the TCR-CD3 complex on T-lymphocyte cell surfaces and play essential roles in adaptive immune response by transmitting TCR-mediated signals across the cell membrane through immunoreceptor tyrosine-based activation motifs (ITAMs). This antibody forms a complex with the CD3 epsilon/delta ectodomain heterodimer.", "target_protein": "EVQLQQSGPELVKPGASMKISCKASMNWVKQSHGKNLEWMGLTYNQKFKDKATLTVDKSSSTAYMELLSLTSEDSAVYYCWGQGTTLTVFSGYSFTGYTINPYKGVSARSGYYGDSDWYFDV", "metadata": {"pdb_id": "1xiw", "light_chain_seq": "DIQMTQTTSSLSASLGDRVTISCRASQDIRNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSKFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFAGGTKLEI", "cdrh1_seq": "GYSFTGYT", "cdrh2_seq": "INPYKGVS", "cdrh3_seq": "ARSGYYGDSDWYFDV", "cdrl1_seq": "QDIRNY", "cdrl2_seq": "YTS", "cdrl3_seq": "QQGNTLPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "1xiw", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "UCHT1", "antibody_format": "scFv", "heavy_subclass": "IGHV1", "light_subclass": "IGKV10", "is_engineered": false, "target_antigen": "T-cell surface glycoprotein CD3 epsilon chain and CD3 delta chain, Homo sapiens", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 7135, 2957, 17, 4659, 11417, 12, 19863, 13, 16, 24314, 6613, 12, 20733, 7390, 19, 7021, 1040, 7390, 1008, 17, 12093, 13, 16, 5133, 1920, 9016, 22206, 19, 9649, 15672, 1927, 1920, 2616, 62, 17, 2024, 3154, 11424, 9016, 2796, 18, 1920, 9016, 22206, 1930, 9649, 7835, 2032, 3131, 1927, 1920, 8367, 17, 9016, 2796, 1990, 62, 17, 10009, 2024, 7553, 1930, 3918, 4415, 5456, 1922, 7617, 3743, 2644, 2007, 27622, 8367, 17, 3434, 4771, 3436, 1920, 2024, 3260, 2596, 8613, 3342, 1924, 6941, 17, 2454, 2936, 8277, 12, 2176, 4645, 13, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 9016, 22206, 19, 9649, 27385, 15672, 18, 3], "antigen": ["QTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVC", "MKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDLGKRILDPRGIYRCNESTVQVHYRMCQS"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A murine Fab, H5M9 (IGHV1/IGKV3-Kappa), targeting the Hemagglutinin of Influenza A virus (H5N1). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and serves as a class I viral fusion protein responsible for penetrating the virus into the cell cytoplasm. The antibody is designed as a broadly neutralizing antibody against diverse H5N1 clades and subclades, targeting a conserved epitope in the HA1 vestigial esterase subdomain that is distinct from the receptor binding site.", "target_protein": "EVHLQQSGPELVKPGASVKMSCKTSIHWMKQSHGKSLEWIGGTYNQKFKVRATLTVGRSSSTAYMDLRSLTSEDSAVYYCWGAGTTVTVSSAGYTFTEYTIFPNNGDTVRNYGSSYGYFDV", "metadata": {"pdb_id": "4mhj", "light_chain_seq": "DIVLTQSPGSLTVSLGQRATISCRASESVDNFGKSFMHWYQQKPGQSPKLLIYRASNREGIPARFNGSGSGTDFALTINPVEADDVATYFCQQSNEDPRTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTEYT", "cdrh2_seq": "IFPNNGDT", "cdrh3_seq": "VRNYGSSYGYFDV", "cdrl1_seq": "ESVDNFGKSF", "cdrl2_seq": "RAS", "cdrl3_seq": "QQSNEDPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[91, 99]", "cdrh3_split": "val", "cdrh3_cluster": "8g5b", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "H5M9", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing murine monoclonal antibody, H5M9, to most H5N1 clades and subclades"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 7135, 6914, 16, 14106, 1035, 1026, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 12, 20128, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 10634, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 19879, 1920, 3413, 2460, 1920, 2024, 5239, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 3316, 6445, 20128, 15961, 1930, 8959, 6363, 16, 5133, 43, 5305, 10095, 1922, 1920, 2118, 1009, 5634, 2677, 2086, 26389, 27517, 1988, 1977, 4493, 2037, 1920, 3148, 2743, 3200, 18, 3], "antigen": ["PGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKASPANDLCYPGDFNDYEELKHLLSRTNHFEKIQIIPKSSWSNHDASSGVSSACPYHGRSSFFRNVVWLIKKNSAYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPEIATRPKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSAIMKSELEGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNTP"]} {"modality_type": "antibody", "text": "I want an antibody that has the function: A human Fab, PGZL1 (IGHV1/IGKV3-Kappa), targeting the Envelope glycoprotein gp41 of Human immunodeficiency virus 1. The Envelope glycoprotein gp41 mediates fusion of viral and host cell membranes during entry. The antibody is designed as a broadly neutralizing antibody targeting the membrane-proximal external region (MPER), with a short CDRH3 and low polyreactivity, engaging the MPER epitope on the viral membrane. Output the HCDRs.", "target_protein": "QVQLVQSGAEVKKPGSSVKVSCKASISWVRQAPGQGLEWMGGNYAQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCWGQGTVITVSSAGGTFSSYAIIPIFGTAAREGEGWFGKPLRAFEF", "metadata": {"pdb_id": "6o41", "light_chain_seq": "IVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGTSQSTFGQGTRLEIKRT", "cdrh1_seq": "GGTFSSYA", "cdrh2_seq": "IIPIFGTA", "cdrh3_seq": "AREGEGWFGKPLRAFEF", "cdrl1_seq": "QSVSSSY", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYGTSQST", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[25, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6mto", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "PGZL1", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp41, Human immunodeficiency virus 1", "target_domain": "Membrane-proximal external region (MPER)", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibody from an HIV-infected person that recognizes the membrane-proximal external region (MPER) of HIV envelope glycoprotein"}}}, "tokenized_instruction": [2, 51, 12914, 1925, 3533, 1988, 2258, 1920, 2347, 30, 43, 2616, 6914, 16, 5306, 26262, 1009, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 25618, 1927, 2616, 13141, 3413, 21, 18, 1920, 11262, 11424, 25618, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 16, 1956, 43, 3662, 20170, 18649, 1930, 2330, 4286, 1936, 5454, 16, 15888, 1920, 5438, 1915, 10095, 1990, 1920, 4324, 3260, 18, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["VTTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEHHH"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A murine Fab, vFP7.04 (IGHV1/IGKV1-Kappa), targeting the Fusion peptide (residues 512-519) of the Envelope glycoprotein gp160 from Human immunodeficiency virus 1. The fusion peptide is a critical component of the viral entry machinery that mediates fusion of viral and host cell membranes. The antibody is designed as a vaccine-elicited neutralizing antibody targeting the exposed N-terminal residues of the fusion peptide to achieve cross-clade neutralization of diverse HIV-1 strains, binding within the Fusion peptide.", "target_protein": "QVQLQQSGAELVRPGASVTLSCKASMHWVKQTPVHGLEWIGAAYTQKFKGKAMLTADKSSSTAYMELRSLTSEDSAVYFCWGTGTTVTVSSAGYTFTDYEIVPETGFTSRLRLYWYFDV", "metadata": {"pdb_id": "6cdm", "light_chain_seq": "GVLMTQTPLSLPVRLGDQASISCRSSQSIVYSNGNTYLEWYLQRPGQSPKLLIYKVSNRFSGVPDRVSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKRT", "cdrh1_seq": "GYTFTDYE", "cdrh2_seq": "IVPETGFT", "cdrh3_seq": "SRLRLYWYFDV", "cdrl1_seq": "QSIVYSNGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQGSHVPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "6cdm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "vFP7.04", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "HIV fusion peptide (512-519), Human immunodeficiency virus 1", "target_domain": "Fusion peptide", "functional_role": "neutralizing", "evidence_quote": "vaccine-elicited antibodies capable of neutralizing diverse primary isolates of HIV-1"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 15691, 1034, 1027, 18, 5228, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 5289, 4207, 12, 4248, 20094, 17, 29636, 13, 1927, 1920, 11262, 11424, 4882, 16954, 2037, 2616, 13141, 3413, 21, 18, 1920, 5289, 4207, 1977, 43, 4140, 4594, 1927, 1920, 4324, 6904, 10853, 1988, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 18, 1920, 3533, 1977, 4609, 1966, 43, 5955, 17, 9856, 12130, 3533, 5133, 1920, 4616, 56, 17, 4262, 4248, 1927, 1920, 5289, 4207, 1942, 6230, 3567, 17, 11315, 14377, 1927, 6445, 3525, 17, 21, 4046, 16, 2743, 2651, 1920, 5289, 4207, 18, 3], "antigen": ["AVGIGA"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A human Fab, RUPA-32 (IGHV3/IGKV3-Kappa), targeting the engineered Gametocyte surface protein P230 of Plasmodium falciparum. Gametocyte surface protein P230 is required for male/female gamete fusion, male gamete exflagellation, and interaction with host erythrocytes. The antibody is designed to block parasite transmission to mosquitoes via complement-dependent mechanisms, targeting a highly conserved epitope on Pfs230 domain 1 that is recognized by naturally acquired antibodies with potent transmission-reducing activity. Generate the corresponding HCDRs.", "target_protein": "EVQLVESGGGLVKPGGSLRLSCAASMSWVRQAPGKGLEWVSSYYTDSVKGRFTISRDNAKKSLFLHMNSLRAEDTAVYYCWGQGARVTVSSAGFAFSTYAISESSSYTARSDGLSMIAAPFDY", "metadata": {"pdb_id": "7uvh", "light_chain_seq": "EIVLTQSPATLSLSPGERATLSCRTSQSLSISLVWYQQKPGQAPRLLISDASNRAPGIPARFSASGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPITFGQGTRLEMKRT", "cdrh1_seq": "GFAFSTYA", "cdrh2_seq": "ISESSSYT", "cdrh3_seq": "ARSDGLSMIAAPFDY", "cdrl1_seq": "QSLSIS", "cdrl2_seq": "DAS", "cdrl3_seq": "QQRSNWPPIT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "7uvh", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "RUPA-32", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Gametocyte surface protein P230, Plasmodium falciparum", "target_domain": null, "functional_role": "other", "evidence_quote": "potently block parasite transmission to mosquitoes; complement-dependent transmission-reducing activity"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 7212, 4302, 17, 3323, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 21009, 4463, 3154, 2213, 7535, 4294, 1927, 15663, 13098, 18, 21009, 4463, 3154, 2213, 7535, 4294, 1977, 3414, 1958, 4005, 19, 4232, 21009, 1021, 5289, 16, 4005, 21009, 1021, 1975, 20631, 30439, 16, 1930, 2835, 1956, 4423, 14161, 18, 1920, 3533, 1977, 4609, 1942, 3367, 8652, 5303, 1942, 13667, 3454, 5508, 17, 3100, 3531, 16, 5133, 43, 3626, 5305, 10095, 1990, 11133, 4553, 1008, 3418, 21, 1988, 1977, 6783, 2007, 10414, 5815, 3788, 1956, 6828, 5303, 17, 5526, 2455, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["TESGDTAVSEDSYDKYASQNTNKEYVCDFTDQLKPTESGPKVKKCEVKVNEPLIKVKIICPLKGSVEKLYDNIEYVPKKSPYVVLTKEETKLKEKLLSKLIYGLLISPTVNEKENNFKEGVIEFTLPPVVHKATVFYFICDNSKTEDDNKKGNRGIVEVYVEPYG"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A murine Fab, D6.3 (IGHV1/IGKV3-Kappa), targeting the engineered core fragment of Envelope glycoprotein H of Suid herpesvirus 1 (pseudorabies virus). The Envelope glycoprotein H, as part of the heterodimer gH/gL, is required for fusion of viral and plasma membranes leading to virus entry into the host cell, working together with glycoprotein B and the gH/gL heterodimer to mediate membrane fusion. This antibody forms a complex with the Envelope glycoprotein H core fragment.", "target_protein": "QVQLQQPGAELVKPGASVKMSCKASMNWVKQRPGRGLEWIGRHYNQDFKDKVTLTVDKSSSTVYIQLSSLTSEDSAVYYCWGQGTTLTVSSAGYSFTSYWIDPSDNETGRLGYVYGFDY", "metadata": {"pdb_id": "2xqy", "light_chain_seq": "DIVLTQSPASLALSLGQRATISCRASKSVSTSGYSYMYWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSGTDFTLNIHPVEEEDAATYYCQHSRELPWTFGGGTKLEINRA", "cdrh1_seq": "GYSFTSYW", "cdrh2_seq": "IDPSDNET", "cdrh3_seq": "GRLGYVYGFDY", "cdrl1_seq": "KSVSTSGYSY", "cdrl2_seq": "LAS", "cdrl3_seq": "QHSRELPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "2xqy", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "D6.3", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Envelope glycoprotein H, Suid herpesvirus 1", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 7135, 6914, 16, 15304, 18, 23, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 4728, 5302, 1927, 11262, 11424, 50, 1927, 2020, 1960, 25718, 21, 12, 11520, 5524, 3821, 1918, 3413, 13, 18, 1920, 11262, 11424, 50, 16, 1966, 3131, 1927, 1920, 15672, 6101, 19, 2393, 16, 1977, 3414, 1958, 5289, 1927, 4324, 1930, 3582, 5726, 4523, 1942, 3413, 6904, 2460, 1920, 4423, 2024, 16, 5905, 4084, 1956, 11424, 44, 1930, 1920, 6101, 19, 2393, 15672, 1942, 8265, 3260, 5289, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 11262, 11424, 50, 4728, 5302, 18, 3], "antigen": ["GVRRTYTTAAVWPAEVAVLADAEARCPAAVFNVTLGEAFLGLRVALRSFLPLEVIISAERMRMIAPPGRFHVYTLGFLSDGAMHQTMRDVAAYVHESDDYLAQLSAAHAAALAAVVQPGPYYFYRAAVRLGVAAFVFSEAARRDRRASAPALLRVESDARLLSRLLMRAAGCPAGFAGLFDGRAERVPVAPADQLRAAWTFGEDPAPRLDLARATVAEAYRRSVRGKPFDQQALFFAVALLLRAGGPGDARETLLRTTAMCTAERAAAAAELTRAALSPTAAWNEPFSLLDVLSPCAVSLRRDLATLANLGAAARLALAPAGEEEDPVARAAPEIPAEALLALPLRGGASFVFTRRRPDCGPAYTLGGVDIANPLVLAIVSNCDYTDRMPESQHLPATDNPSVCVYCDCVFVRYSSAGTILETVLIESKDMEEQLMAGPSFNPTLHGGDVKALMLFPNGTVVDL"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human Fab, PN-SIA28 (IGHV3/IGKV1-Kappa), targeting the Hemagglutinin of Influenza A virus. Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for membrane fusion by undergoing conformational changes in acidic endosomes. The antibody is designed as a broadly neutralizing antibody targeting the conserved stem region of HA, capable of neutralizing divergent group 1 and group 2 influenza A subtypes including endemic strains and emerging bat influenza viruses, by inhibiting HA-mediated membrane fusion and blocking HA0 maturation. Please generate the HCDRs for this antibody.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVAGYYADSVKGRFTISRDSSKSTLYLQMNSLRPEDTAVYYCWGQGTTVTVSGFPFSSYGVSYDGSYKARPSAIFGIYIILNGLDV", "metadata": {"pdb_id": "8gv5", "light_chain_seq": "EIVLTQSPSSVSASVGDRVTITCRATQGISSWLAWYQQKPGKPPKLLIFGASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYFCQQAHSFPLTFGGGTKVEIK", "cdrh1_seq": "GFPFSSYG", "cdrh2_seq": "VSYDGSYK", "cdrh3_seq": "ARPSAIFGIYIILNGLDV", "cdrl1_seq": "QGISSW", "cdrl2_seq": "GAS", "cdrl3_seq": "QQAHSFPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7wvd", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "PN-SIA28", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": "stem region", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing activity against group 1 and group 2 IAV strains"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 7594, 17, 26352, 4839, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 3260, 5289, 2007, 7258, 8523, 2840, 1922, 9931, 14978, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 5305, 4402, 3031, 1927, 2118, 16, 7131, 1927, 12130, 13609, 2210, 21, 1930, 2210, 22, 7108, 43, 8160, 2710, 12310, 4046, 1930, 8484, 11579, 7108, 6241, 16, 2007, 7918, 2118, 17, 3434, 3260, 5289, 1930, 7472, 2118, 1008, 7655, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["GAIAGFIEGGWTGMIDGWYGYHHQNEHGSGYAADQKSTQIAIDGIRNKVNSVIEKMNIQFTSVGKEFNSLEKRMENLNKKVDDGFLDVWTYNAELLILLENERTLDYHDFNVKNLYEKVKSQLRNNAKEIGNGCFEFYHKCDNECMESVKNGTYNYP", "DTICVGYHANNSTDTVDTILEKNVTVTHSVNLLEDSHNGKLCSLNGKSPLQLGNCNVAGWILGNPECDLLLTADSWSYIIETSNSKNGACYPGEFTDYEELREQLSTVSSFERFEIFPKATSWPNHDTTKGTTVACSHSGAKSFYRNLLWIVQKENSYPKLSNSYTNNKGKRVLVIWGVHHPYRDQQALYRNNHTYVSVESSKYYQRFTPEIVARPKVREQAGRINYYWTLLDQGDTITFEATGNLIAPWHAFALKKGSSSGMMVSDAQVHNCTTKCQTPHGALKSNLPFQNVHPITIGECPKYVKSTQLRMATGLRNIPS"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human Fab, SD4 (IGHV3/IGKV1-Kappa), targeting the engineered Envelopment polyprotein (Gn) of SFTS virus JS4. The Envelopment polyprotein is a structural component of the virion that acts as a class II fusion protein, attaches the virion to the host cell receptor CD209/DC-SIGN, and promotes fusion of membranes with the late endosome after clathrin-mediated endocytosis. The antibody is designed as a neutralizing antibody with broad-spectrum activity against diverse SFTSV genotypes, targeting a conserved epitope in the Gn head domain A that prevents virus binding to host cell receptors. What would the HCDRs be?", "target_protein": "VQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVAVNYADSVKGRFTISRDNSKNTLYLQMNSLRVEDTAVYYCWGQGTLVTVSSAGFPFSGYGISYDGSEKAKDRDYYGSGFYDY", "metadata": {"pdb_id": "9jqu", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCQASQHISNHLNWYQQKPGTAPTLLIYEASNLETGVPSRFSGSGSGTDFSFTISSLRPEDFATYYCQQYDNFPLTFGPGTTMDIKRT", "cdrh1_seq": "GFPFSGYG", "cdrh2_seq": "ISYDGSEK", "cdrh3_seq": "AKDRDYYGSGFYDY", "cdrl1_seq": "QHISNH", "cdrl2_seq": "EAS", "cdrl3_seq": "QQYDNFPLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9l2k", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "SD4", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Envelopment polyprotein (Gn), SFTS virus JS4", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibodies reported in the present study have significant therapeutic potential"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 6914, 16, 4035, 1006, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 9840, 2017, 6240, 5684, 12, 9005, 13, 1927, 6347, 1973, 3413, 16883, 1006, 18, 1920, 9840, 2017, 6240, 5684, 1977, 43, 4346, 4594, 1927, 1920, 19230, 1988, 8016, 1966, 43, 2921, 2890, 5289, 2213, 16, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3148, 16494, 1026, 19, 5330, 17, 2105, 16, 1930, 7383, 5289, 1927, 5726, 1956, 1920, 5058, 22321, 2256, 17053, 17, 3434, 11914, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1956, 4949, 17, 5648, 2455, 3316, 6445, 6347, 1973, 1020, 7059, 16, 5133, 43, 5305, 10095, 1922, 1920, 9005, 4469, 3418, 43, 1988, 10299, 3413, 2743, 1942, 4423, 2024, 4086, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["DSGPIICAGPIHSNKSAGIPHLLGYSEKICQIDRLIHVSSWLRNHSQFQGYVGQRGGRSQVSYYPAENSYSRWSGLLSPCDADWLGMLVVKKARESDMIVPGPSYKGKVFFERPTFDGYVGWGCGSGKSRTESGELCSSDSGTSSGLLPSDRVLWIGDVACQLMTPIPEETFLELKSFSQSEFPDICKIDGIVFNQCEGESLPQPFDVAWMDVGHSHKIIMREHKTKWVQESSSKDFVCYKEGTGPCSESEEKACKTSGSCRGDMQFCKVAGCEHGEETSEAKCRCSLVHKPGEVVVSYGGMRVRPKCYGFSRMMATLHHH"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A human Fab (IGHV4/IGKV1-Kappa) targeting the engineered Spike glycoprotein of Human coronavirus HKU1 (isolate N1). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptor TMPRSS2 to initiate infection, and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that blocks the RBD:TMPRSS2 interaction to prevent viral entry, binding within the BetaCoV S1-CTD.", "target_protein": "QVQLQESGPGLVKPSGTLSLTCAVSWSWVRQPPGKGLEWIGSHYKPSLKSRIAMSVDTSKNQFSLNLNSVTAADTAVYYCWGQGTTVTVSSAGGSISSSNWMHYSGSSAREGGSSGYDYVYYFDD", "metadata": {"pdb_id": "9jcy", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPRTFGQGTKVEIKRT", "cdrh1_seq": "GGSISSSNW", "cdrh2_seq": "MHYSGSS", "cdrh3_seq": "AREGGSSGYDYVYYFDD", "cdrl1_seq": "QSISSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSYSTPRT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9jcy", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Human coronavirus HKU1 (isolate N1)", "target_domain": "BetaCoV S1-CTD", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibodies that disrupt the RBD:TMPRSS2 interaction could block viral entry"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11091, 10429, 11424, 1927, 2616, 5548, 10703, 13595, 24396, 12, 9158, 13007, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 3148, 23992, 5675, 13262, 1942, 11051, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 1920, 25780, 30, 23992, 5675, 13262, 2835, 1942, 4625, 4324, 6904, 16, 2743, 2651, 1920, 4666, 4879, 1020, 4062, 17, 15898, 18, 3], "antigen": ["DLPDCDIDKWLNNFNVPSPLNWERKIFSNCNFNLSTLLRLVHTDSFSCNNFDESKIYGSCFKSIVLDKFAIPNSRRSDLQLGSSGFLQSSNYKIDTTSSSCQLYYSLPAINVTINNYNPSSWNRRYGFNNFNLSSHSVVYSRYCFSVNNTFCPCAKPSFASSCKSHKPPSASCPIGTNYRSCESTTVLDHTDWCRCSCLPDPITAYDPRSCSQKKSLVGVGEHCAGFGVDEEKCGVLDGSYNVSCLCSTDAFLGWSYDTCVSNNRCNIFSNFILNGINSGTTCSNDLS"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A human Fab, 2D1 (IGHV2/IGLV1-Lambda), targeting the Hemagglutinin HA1 Subunit of Influenza A virus (1918 H1N1 strain). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for membrane fusion during infection. The antibody is designed as a neutralizing antibody that recognizes a conserved epitope present in both 1918 and 2009 H1N1 pandemic viruses.", "target_protein": "VQLVESGPALVKPTQTLTLTCSFSVSWIRQPPGKALEWLALTYSSSLKTRLTISKDTSKSQVVLTMTNMDPVDTATYYCWGRGTLVTVSSAGFSLSTSGMSIDWDDDTYYIARTLRVSGDYVRDFDL", "metadata": {"pdb_id": "3lzf", "light_chain_seq": "PVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVSWYQQVPGTAPKLLIYGNNERPSGVPDRFSGSKSATSASLAISGLQSEDEADYYCAAWDDSLNGFWVFGGGTKLTVLGQ", "cdrh1_seq": "GFSLSTSGMS", "cdrh2_seq": "IDWDDDTYYI", "cdrh3_seq": "ARTLRVSGDYVRDFDL", "cdrl1_seq": "SSNIGSNT", "cdrl2_seq": "GNN", "cdrl3_seq": "AAWDDSLNGFWV", "cdrh1_pos": "[24, 33]", "cdrh2_pos": "[51, 60]", "cdrh3_pos": "[99, 114]", "cdrl1_pos": "[24, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 99]", "cdrh3_split": "val", "cdrh3_cluster": "3lzf", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2D1", "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "Hemagglutinin, HA1 Subunit, Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizes both 1918 and 2009 H1N1 viruses"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 5941, 1009, 12, 20733, 15755, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 26141, 2118, 1009, 5903, 1927, 7108, 43, 3413, 12, 18162, 1025, 15355, 3943, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 3260, 5289, 2409, 2909, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 16197, 43, 5305, 10095, 2481, 1922, 2321, 18162, 1025, 1930, 3712, 15355, 16913, 6241, 18, 3], "antigen": ["DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPS"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human Fab targeting an engineered variant of Tyrosine-protein phosphatase non-receptor type substrate 1 (SIRP\u03b1), a human immunoglobulin-like cell surface receptor for CD47 that mediates negative regulation of phagocytosis and dendritic cell activation. This non-blocking anti-SIRP\u03b1 antibody is designed to enhance macrophage-mediated antibody-dependent cellular phagocytosis of tumor cells, binding within the Ig-like V-type domain. The antibody should bind both human SIRP\u03b1 v1 and v2 alleles with high affinity and cross-react with cynomolgus and mouse SIRP\u03b1 alleles to enable preclinical and clinical development. What would the HCDRs be?", "target_protein": "AVTLDESGGGLQTPGGALSLVCKASMNWVRQAPGKGLEFVAQYYGAAVKGRATISRDNRQSTVKLQLNNLRAEDTGIYFCWGNGTEVIVSSAGFIFSDYGITSGSRTARDFGSGVGSIDA", "metadata": {"pdb_id": "6nmt", "light_chain_seq": "ALTQPASVSANLGGTVKITCSGSRGRYGWYQQRSPGSAPVTVIYRDNQRPSNIPSRFSSSTSGSTSTLTITGVQADDESVYFCGSYDGSIDIFGAGTTLTVLRT", "cdrh1_seq": "GFIFSDYG", "cdrh2_seq": "ITSGSRT", "cdrh3_seq": "ARDFGSGVGSIDA", "cdrl1_seq": "RGRYG", "cdrl2_seq": "RDN", "cdrl3_seq": "GSYDGSIDI", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 107]", "cdrl1_pos": "[23, 27]", "cdrl2_pos": "[44, 46]", "cdrl3_pos": "[83, 91]", "cdrh3_split": "val", "cdrh3_cluster": "6nmt", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": null, "light_subclass": null, "is_engineered": true, "target_antigen": "Tyrosine-protein phosphatase non-receptor type substrate 1 (SIRP\u03b1), Homo sapiens", "target_domain": "Ig-like V-type", "functional_role": "other", "evidence_quote": "non-blocking anti-SIRP\u03b1 antibodies enhance macrophage phagocytosis of tumor cells"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 6914, 5133, 1925, 11091, 6031, 1927, 6941, 17, 2213, 8167, 2447, 17, 3148, 2601, 4510, 21, 12, 4520, 1034, 1071, 13, 16, 43, 2616, 11837, 17, 3189, 2024, 3154, 3148, 1958, 29741, 1988, 10412, 3136, 3640, 1927, 13715, 1930, 8104, 2024, 2936, 18, 2052, 2447, 17, 7472, 2246, 17, 4520, 1034, 1071, 3533, 1977, 4609, 1942, 4826, 8088, 17, 3434, 3533, 17, 3100, 3689, 13715, 1927, 2798, 2094, 16, 2743, 2651, 1920, 7021, 17, 3189, 64, 17, 2601, 3418, 18, 1920, 3533, 3066, 4566, 2321, 2616, 4520, 1034, 1071, 11217, 1930, 12701, 7096, 1956, 2149, 5173, 1930, 3567, 17, 9793, 1956, 23836, 30351, 13057, 1930, 3321, 4520, 1034, 1071, 7096, 1942, 8675, 10311, 1930, 2535, 2740, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["EEELQVIQPDKSVLVAAGETATLRCTATSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRIGAITPADAGTYYCVKFRKGSPDDVEFKSGAGTELSVR"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab (IGHV3/IGKV1-Kappa), one of three antibodies in a triple-antibody complex (S309, S2L20, S2X303), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (C.37 Lambda variant). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding and proteolytic cleavage. This antibody forms a complex with the Spike glycoprotein. Please output the HCDRs.", "target_protein": "EVQLVESGGGVVQPGGSLRLSCAASMHWVRQAPGKGLEWVAFYYADSVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCWGQGTLVTVSGFTFNSYGIRYDGGNKANLKDSRYSGSYYDY", "metadata": {"pdb_id": "8vye", "light_chain_seq": "VIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKVDFK", "cdrh1_seq": "GFTFNSYG", "cdrh2_seq": "IRYDGGNK", "cdrh3_seq": "ANLKDSRYSGSYYDY", "cdrl1_seq": "QDIRFY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYDNLPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9c44", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 2340, 1927, 2559, 3788, 1922, 43, 10073, 17, 3533, 2796, 12, 6080, 13192, 16, 5159, 11232, 1008, 16, 5159, 12001, 12962, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 45, 18, 3191, 18279, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 1930, 12712, 6404, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 11424, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["QCVNLRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHNSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVCPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYQYRLFRKSNLKPFERDISTEIVEGFNCYSPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVQKFNGLNVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLCPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPEL"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human Fab, DH511.12P (IGHV3/IGKV1-Kappa), targeting the membrane-proximal external region (MPER) peptide of HIV-1 gp41. The gp41 MPER is part of the envelope glycoprotein that mediates fusion of viral and host cell membranes during entry. The antibody is designed as a broadly neutralizing antibody targeting the distal MPER, binding within the MPER domain and recognizing a transiently exposed intermediate conformation of gp41 that is exposed during the virion-host cell fusion process. Can you generate its HCDRs?", "target_protein": "QVQLVQSGGGLVKPGGSLTPSCVTSMSWVRQTPGKGLEWVARDYAAPVKGRFIISRDDSRNTLFLHMNNLKTEDTAVYYCWGKGTTVIVSSAGFTFSNTWISRVGDGPIITADEGAPILRFFEWGYYNYYMDV", "metadata": {"pdb_id": "5u3n", "light_chain_seq": "DIRLTQSPSSLSASVGDRITITCRASQSIKDYLNWYKHRPGEAPKLLIYSASKLRSGVSSRFSGSGYGSAFTLTISSLQPEDFATYYCQESYSSVPMYIFGQGTKVDLKRT", "cdrh1_seq": "GFTFSNTW", "cdrh2_seq": "ISRVGDGPII", "cdrh3_seq": "TADEGAPILRFFEWGYYNYYMDV", "cdrl1_seq": "QSIKDY", "cdrl2_seq": "SAS", "cdrl3_seq": "QESYSSVPMYI", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 120]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "5u3m", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DH511.12P", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "gp41 MPER peptide, Human immunodeficiency virus 1", "target_domain": "MPER; binding to GalCer", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing distal MPER bnAbs...potently neutralized most HIV-1 strains"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 6914, 16, 6781, 7912, 1009, 18, 25080, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 4207, 1927, 3525, 17, 21, 25618, 18, 1920, 25618, 5438, 1915, 1977, 3131, 1927, 1920, 11262, 11424, 1988, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 6583, 5438, 1915, 16, 2743, 2651, 1920, 5438, 1915, 3418, 1930, 15667, 43, 12145, 4616, 6129, 7748, 1927, 25618, 1988, 1977, 4616, 2409, 1920, 19230, 17, 4423, 2024, 5289, 2585, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["ELDKWASLWNWFDITNWLWYIRK"]} {"modality_type": "antibody", "text": "I want an antibody that has the function: A human Fab, C135 (IGHV3/IGKV1-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that recognizes a glycopeptidic epitope outside the ACE2 binding site, targeting both up and down RBD conformations on the spike trimer. Output the HCDRs.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVAVYYADSVTGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTLVTVGFTFSSYAIPFDGRNKASSSGYLFHSDY", "metadata": {"pdb_id": "7k8z", "light_chain_seq": "DIQMTQSPSTLSASVGDRVTITCRASQSISNWLAWFQQKPGKAPKLLIYEASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYNSYPWTFGQGTKVEI", "cdrh1_seq": "GFTFSSYA", "cdrh2_seq": "IPFDGRNK", "cdrh3_seq": "ASSSGYLFHSDY", "cdrl1_seq": "QSISNW", "cdrl2_seq": "EAS", "cdrl3_seq": "QQYNSYPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7k8z", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "C135", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "C135 is a potent hNAb that showed binding properties distinct from class 1, class 2, and class 4 hNAbs"}}}, "tokenized_instruction": [2, 51, 12914, 1925, 3533, 1988, 2258, 1920, 2347, 30, 43, 2616, 6914, 16, 8817, 5798, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 16197, 43, 8821, 3173, 1935, 10095, 7008, 1920, 8298, 1028, 2743, 3200, 16, 5133, 2321, 2353, 1930, 3292, 25780, 12526, 1990, 1920, 10429, 20085, 18, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVNCTFEYVSFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKNYNYLYRLFRKSNLKPFERDISTFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNEVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKSKRSFIEDLLFNKVTNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A human Fab, H014 (IGHV1/IGKV6-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors (primarily ACE2) and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding. The antibody is designed as a neutralizing antibody that prevents attachment of SARS-CoV-2 to host cell receptors, targeting a conformational epitope accessible when the RBD is in the open state within the trimeric spike.", "target_protein": "VQLVQSGAEVKKPGATVKISCKVSIHWVKQAPGKSLEWIGYSDNLKFKGAATLTADTSTDTAYMELSSLRSEDTAVYYCWGQGTTVTVSSAGYSFSNYYIDPFNGGTARSEYDPYYVMDY", "metadata": {"pdb_id": "7cac", "light_chain_seq": "IVLTQSPFQSVSPKEKVTITCRASQSISSNLHWYQQKPDQSPKLLIKYASQSISGIPSRFSGSGSGTDFTLTINSLEAEDFGIYFCQQTNFWPYIFGQGTKLEILKR", "cdrh1_seq": "GYSFSNYY", "cdrh2_seq": "IDPFNGGT", "cdrh3_seq": "ARSEYDPYYVMDY", "cdrl1_seq": "QSISSN", "cdrl2_seq": "YAS", "cdrl3_seq": "QQTNFWPYI", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 107]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "7cak", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "H014", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "efficiently neutralizes SARS-CoV-2 and SARS-CoV by engaging the spike RBD"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 2616, 6914, 16, 29161, 3745, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 12, 5985, 8298, 1028, 13, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 10299, 8576, 1927, 20466, 17, 6083, 17, 22, 1942, 4423, 2024, 4086, 16, 5133, 43, 8523, 10095, 10551, 2469, 1920, 25780, 1977, 1922, 1920, 4437, 3360, 2651, 1920, 29177, 10429, 18, 3], "antigen": ["PPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTMAYRFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human Fab, SD22 (IGHV3/IGKV1-Kappa), targeting the engineered Envelopment polyprotein (Gn head domain A) of Severe fever with thrombocytopenia syndrome virus. The antibody is designed as a neutralizing antibody with broad-spectrum activity against multiple SFTSV genotypes (J1, J3, C2, C3), achieving picomolar binding affinity and demonstrating therapeutic efficacy in rescuing mice from lethal SFTSV challenge. SD22 prevents virus binding to host cells by targeting a conserved epitope on the Gn head.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVALYYSDSVKGRFTISRDNSKNTLYLQLKSLRPDDTAVYYCWGQGTLVTVSSGFTFSGFGISYDGSDTVGDRDYFGSGFFDH", "metadata": {"pdb_id": "9l2k", "light_chain_seq": "DIQMTQSPSSLSASIGDRVTITCRASRHITNHLNWYQHKPGRAPKLLIYEASNLQAGVPSRFSGSGSGTDFTFTISSLQPEDFATYYCQQYDNLPPAFGGGTKVDIKR", "cdrh1_seq": "GFTFSGFG", "cdrh2_seq": "ISYDGSDT", "cdrh3_seq": "VGDRDYFGSGFFDH", "cdrl1_seq": "RHITNH", "cdrl2_seq": "EAS", "cdrl3_seq": "QQYDNLPPA", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9l2k", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "SD22", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Envelopment polyprotein, Severe fever with thrombocytopenia syndrome virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "panel of anti-SFTSV Gn monoclonal antibodies with excellent neutralizing capacities and remarkable therapeutic potential"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 6914, 16, 4035, 4460, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 9840, 2017, 6240, 5684, 12, 9005, 4469, 3418, 43, 13, 1927, 4010, 9087, 1956, 17100, 4741, 3413, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1956, 4949, 17, 5648, 2455, 3316, 3137, 6347, 1973, 1020, 7059, 12, 52, 1009, 16, 52, 1010, 16, 8453, 16, 8351, 13, 16, 11058, 28609, 12492, 5148, 1005, 2743, 5173, 1930, 7530, 4272, 4348, 1922, 7615, 13768, 2518, 2037, 10470, 6347, 1973, 1020, 6013, 18, 4035, 4460, 10299, 3413, 2743, 1942, 4423, 2094, 2007, 5133, 43, 5305, 10095, 1990, 1920, 9005, 4469, 18, 3], "antigen": ["DSGPIICAGPIHSNKSAGIPHLLGYSEKICQIDRLIHVSSWLRNHSQFQGYVGQRGGRSQVSYYPAENSYSRWSGLLSPCDADWLGMLVVKKARESDMIVPGPSYKGKVFFERPTFDGYVGWGCGSGKSRTESGELCSSDSGTSSGLLPSDRVLWIGDVACQLMTPIPEETFLELKSFSQSEFPDICKIDGIVFNQCEGESLPQPFDVAWMDVGHSHKIIMREHKTKWVQESSSKDFVCYKEGTGPCSESEEKACKTSGSCRGDMQFCKVAGCEHGEETSEAKCRCSLVHKPGEVVVSYGGMRVRPKCYGFSRMMATLHHH"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A murine Fab, 22NS1 (IGHV1/IGKV12-Kappa), targeting the Non-structural protein NS1 of West Nile virus. NS1 is a conserved, membrane-associated and secreted glycoprotein with replication and immune evasion functions; secreted NS1 assembles as a hexameric, barrel-shaped lipoprotein that can bind back to the plasma membrane of cells. The antibody is designed as a protective antibody targeting cell surface-associated NS1 in a manner dependent on Fc effector functions.", "target_protein": "QVQLQQPGAELVKPGASVKLSCKASMHWVKLRPGQGFEWIGDSYNEKFKRKATLTVDTSSSTAYMQLSSLTSEDSAVYYCWGQGTLVTVSAAGYTFTSYWINPNNGGPTIDDGYRFGY", "metadata": {"pdb_id": "4oii", "light_chain_seq": "DIQMTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSASGSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTSYW", "cdrh2_seq": "INPNNGGP", "cdrh3_seq": "TIDDGYRFGY", "cdrl1_seq": "GNIHNY", "cdrl2_seq": "NAK", "cdrl3_seq": "QHFWSTPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 105]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "4oii", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "22NS1", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV12", "is_engineered": false, "target_antigen": "Non-structural protein NS1, West Nile virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "protective 22NS1 antibody Fab"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 2950, 3355, 1009, 12, 20733, 7390, 19, 7021, 1040, 7390, 1028, 17, 12093, 13, 16, 5133, 1920, 2447, 17, 4346, 2213, 19082, 1927, 9195, 25624, 3413, 18, 19082, 1977, 43, 5305, 16, 3260, 17, 2458, 1930, 8366, 11424, 1956, 5158, 1930, 3743, 25092, 4088, 31, 8366, 19082, 17421, 1036, 1966, 43, 25602, 1935, 16, 19560, 17, 9132, 9694, 1988, 2112, 4566, 3231, 1942, 1920, 3582, 3260, 1927, 2094, 18, 1920, 3533, 1977, 4609, 1966, 43, 6337, 3533, 5133, 2024, 3154, 17, 2458, 19082, 1922, 43, 5222, 3100, 1990, 6437, 7917, 4088, 18, 3], "antigen": ["TTECDSKIIGTAVKNNLAIHSDLSYWIESRLNDTWKLERAVLGEVKSCTWPETHTLWGDGILESDLIIPVTLAGPRSNHNRRPGYKTQNQGPWDEGRVEIDFDYCPGTTVTLSESCGHRGPATRTTTESGKLITDWCCRSCTLPPLRYQTDSGCWYGMEIRPQRHDEKTLVQSQVNA"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, 310-7D11 (IGHV3/IGKV2-Kappa), targeting the Hemagglutinin HA1 chain of Influenza A virus. Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for membrane fusion in the endosome. This antibody forms a complex with the Hemagglutinin HA1 chain.", "target_protein": "QVQLVESGGGVVQPGRSLRVSCAASMHWVRQAPGKGLEWVALYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTTVTVSSGFIFSNYGTWYDGRNKARDGFPNCISATCGYAMDV", "metadata": {"pdb_id": "9mqa", "light_chain_seq": "DTVMTQSPLSLPVTPGEPASISCRSSQSLLHSNGYNYLEWYLQKPGQSPQLLIYLGSIRASGVPDRLSGSGSGTDFTLKISRVEAEDVGVYYCMQGLETPFTFGPGTKVEIK", "cdrh1_seq": "GFIFSNYG", "cdrh2_seq": "TWYDGRNK", "cdrh3_seq": "ARDGFPNCISATCGYAMDV", "cdrl1_seq": "QSLLHSNGYNY", "cdrl2_seq": "LGS", "cdrl3_seq": "MQGLETPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "9mqa", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "310-7D11", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Hemagglutinin HA1 chain, Influenza A virus", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 17966, 17, 15868, 3242, 12, 20733, 1020, 1010, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 26141, 2118, 1009, 4659, 1927, 7108, 43, 3413, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 3260, 5289, 1922, 1920, 22321, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 26141, 2118, 1009, 4659, 18, 3], "antigen": ["ICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPMCDEFIRVPEWSYIVERANPANDLCFPGSLNDYEELKHMLSRINHFEKIQIIPKSSWPNHETSLGVSAACPYQGAPSFFRNVVWLIKKNDAYPTIKISYNNTNREDLLILWGIHHSNNAEEQTNLYKNPITYISVGTSTLNQRLAPKIATRSQVNGQRGRMDFFWTILKPDDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSGVEYGHCNTKCQTPVGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLR"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab, M4008_N1, targeting the Envelope glycoprotein gp160 of Human immunodeficiency virus 1. The Envelope glycoprotein gp160 oligomerizes into trimers and is proteolytically cleaved to produce gp120 and gp41; gp120 attaches the virus to host lymphoid cells by binding to the primary receptor CD4 and mediates interactions with chemokine coreceptors. The antibody is designed as a broadly neutralizing antibody targeting the V3 crown vulnerable site, a large exposed protein surface centered at the V3 crown that is accessible in the prefusion closed-form Env trimer. The design objective is to engage the V3 crown hairpin through a \u03b2-sheet interaction with the N-terminal strand, enabling neutralization of diverse HIV-1 strains while remaining sensitive to but not dependent on surrounding glycans.", "target_protein": "QLVQSGAEMKTSGSSVRVSCKDSFRWVRQAPGQGFEWMGGHYAPKFQARMKMTVVESSRTLYMELRSLTSTDTATYFCWGQGTQVTVPSGGFFPYAGVIPADGTKARLQCAGFSCEMDSGPFDL", "metadata": {"pdb_id": "7rai", "light_chain_seq": "DIQMTQSPSTVAAFVGGNVTLSCRTSQGVGNRLAWYQQKPGKPPRLLISRASNRHGGVPARFSGGGSGTIFTLTIKGLQSDDFATFFCQQYYDSRETFGQGSRVMMEK", "cdrh1_seq": "GGFFPYAG", "cdrh2_seq": "VIPADGTK", "cdrh3_seq": "ARLQCAGFSCEMDSGPFDL", "cdrl1_seq": "QGVGNR", "cdrl2_seq": "RAS", "cdrl3_seq": "QQYYDSRET", "cdrh1_pos": "[23, 30]", "cdrh2_pos": "[48, 55]", "cdrh3_pos": "[94, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7rai", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "M4008_N1", "antibody_format": "Fab", "heavy_subclass": "unknown", "light_subclass": "unknown", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus 1", "target_domain": "V3 crown", "functional_role": "neutralizing", "evidence_quote": "bNAb M4008_N1 targets a vulnerable site with about 40% neutralization coverage"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 21397, 23789, 41, 13007, 16, 5133, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 21, 18, 1920, 11262, 11424, 4882, 16954, 13034, 4517, 2460, 28220, 1930, 1977, 12712, 2169, 10246, 1942, 5074, 16102, 1930, 25618, 31, 16102, 5823, 1918, 1920, 3413, 1942, 4423, 11751, 2094, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 1930, 10412, 3719, 1956, 11673, 30435, 3448, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 14307, 18819, 11342, 3200, 16, 43, 3103, 4616, 2213, 3154, 10841, 2019, 1920, 14307, 18819, 1988, 1977, 10551, 1922, 1920, 9328, 2670, 8047, 17, 2386, 11118, 20085, 18, 1920, 3036, 4470, 1977, 1942, 11580, 1920, 14307, 18819, 14565, 2596, 43, 161, 17, 11130, 2835, 1956, 1920, 56, 17, 4262, 5984, 16, 12180, 14377, 1927, 6445, 3525, 17, 21, 4046, 2679, 5719, 4532, 1942, 2308, 2084, 3100, 1990, 7510, 15509, 18, 3], "antigen": ["AENLWVTVYYGVPVWKDAETTLFCASDAEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRR"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab, MOR04357 (IGHV3/IGLV3-Lambda), targeting human Granulocyte-macrophage colony-stimulating factor (GM-CSF). GM-CSF is a cytokine that stimulates the growth and differentiation of hematopoietic precursor cells from various lineages, including granulocytes, macrophages, eosinophils and erythrocytes. The antibody is designed as a neutralizing antibody that blocks GM-CSF receptor engagement. Please output the HCDRs.", "target_protein": "QVQLVESGGGLVQPGGSLRLSCAASMNWVRQAPGKGLEWVSGYYAASVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTFSSYWIENKYAGGATARGFGTDF", "metadata": {"pdb_id": "5c7x", "light_chain_seq": "DIELTQPPSVSVAPGQTARISCSGDSIGKKYAYWYQQKPGQAPVLVIYKKRERFSGSNSGNTATLTISGTQAEDEADYYCSAWGDKGMVFGGGTKLTVLGQ", "cdrh1_seq": "GFTFSSYW", "cdrh2_seq": "IENKYAGGAT", "cdrh3_seq": "ARGFGTDF", "cdrl1_seq": "SIGKKY", "cdrl2_seq": "KK", "cdrl3_seq": "SAWGDKGMV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 105]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 49]", "cdrl3_pos": "[80, 88]", "cdrh3_split": "val", "cdrh3_cluster": "5c7x", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "MOR04357", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "Granulocyte-macrophage colony-stimulating factor, Homo sapiens", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing anti-human GM-CSF antibody"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 2803, 14743, 5798, 1027, 12, 20733, 1020, 1010, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 5133, 2616, 19235, 17, 8088, 8271, 17, 9868, 2991, 12, 5711, 17, 6399, 13, 18, 5711, 17, 6399, 1977, 43, 6137, 1988, 11803, 1920, 2905, 1930, 4155, 1927, 9960, 7897, 2094, 2037, 3425, 10439, 16, 2710, 22144, 16, 5205, 16, 15854, 1930, 14161, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 5711, 17, 6399, 3148, 9577, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["STQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEP"]} {"modality_type": "antibody", "text": "A synthetic Fab (IGHV3/IGKV1-Kappa) targeting the 5'-AMP-activated protein kinase catalytic subunit alpha-1 (AMPK) of Homo sapiens. AMPK is an energy sensor protein kinase that regulates cellular energy metabolism by activating energy-producing pathways and inhibiting energy-consuming processes in response to changes in intracellular ATP levels. The antibody is designed as a structural tool to selectively stabilize and trap the ATP-bound, fully inactive conformation of AMPK, enabling structural characterization of the inactive state and mechanistic understanding of AMPK regulation by adenine nucleotides. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVASSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFNIYYYSIYPYSGSTARYYPYFISYYSKMEAMDY", "metadata": {"pdb_id": "7jhh", "light_chain_seq": "QMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSGPITFGQGTKVEIKRT", "cdrh1_seq": "GFNIYYYS", "cdrh2_seq": "IYPYSGST", "cdrh3_seq": "ARYYPYFISYYSKMEAMDY", "cdrl1_seq": "QSVSSA", "cdrl2_seq": "SAS", "cdrl3_seq": "QQSSSGPIT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "7jhh", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "5'-AMP-activated protein kinase catalytic subunit alpha-1, Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "conformation-specific antibodies to trap ATP-bound AMPK in a fully inactive, dynamic state"}}}, "tokenized_instruction": [2, 43, 6830, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 25, 11, 17, 3681, 17, 4128, 2213, 4016, 6804, 5903, 4595, 17, 21, 12, 9835, 13, 1927, 16350, 27974, 18, 9835, 1977, 1925, 3844, 6443, 2213, 4016, 1988, 7014, 3689, 3844, 4714, 2007, 8019, 3844, 17, 7144, 3873, 1930, 7918, 3844, 17, 12359, 4028, 1922, 2644, 1942, 2840, 1922, 4776, 4498, 2428, 18, 1920, 3533, 1977, 4609, 1966, 43, 4346, 5229, 1942, 9331, 13448, 1930, 10947, 1920, 4498, 17, 4124, 16, 5437, 9078, 7748, 1927, 9835, 16, 12180, 4346, 7285, 1927, 1920, 9078, 3360, 1930, 10640, 4339, 1927, 9835, 3640, 2007, 15643, 9519, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["VKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRATIKDIREHEWFKQDLPKYLFPEDPSHQGVRKAKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTYSKMSLQLYQVDSRTYLLDFRSIDDELTPRPGSHTIEFFEMCANLIKILAQ"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab, CV07-270 (IGHV3/IGLV2-Lambda), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the host cell membrane by interacting with host receptors, initiating infection, and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting the Receptor-binding domain (RBD).", "target_protein": "QVQLVESGGGLVKPGGSLRLSCAASMTWIRQAPGKGLEWVSYYYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTFSDYYISSSGSTIARARGSSGWYRIGTRWGNWFDP", "metadata": {"pdb_id": "6xkp", "light_chain_seq": "ALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYEVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSNVVFGGGTMLTVLGQ", "cdrh1_seq": "GFTFSDYY", "cdrh2_seq": "ISSSGSTI", "cdrh3_seq": "ARARGSSGWYRIGTRWGNWFDP", "cdrl1_seq": "SSDVGGYNY", "cdrl2_seq": "EVS", "cdrl3_seq": "SSYTSSSNVV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 117]", "cdrl1_pos": "[23, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "6xkp", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CV07-270", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV2", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody with IC50 of 82.3 ng/mL against SARS-CoV-2"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 5519, 14099, 17, 16646, 12, 20733, 1020, 1010, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 3], "antigen": ["NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab (IGHV1/IGLV3-Lambda) targeting the transmembrane glycoprotein gp41 of Human immunodeficiency virus 1. The gp41 N-heptad repeat (N-HR) forms a trimeric coiled-coil during viral fusion and is accessible as an attractive target for broadly neutralizing antibodies. The antibody is designed to neutralize HIV-1 by blocking the formation of the six-helix bundle, preventing completion of the fusion process, binding within the N-heptad repeat (N-HR) region. The design should enable multivalent engagement of the N-HR trimer, with up to three antibody molecules binding to equivalent sites on the trimeric surface.", "target_protein": "QLVQSGAEVKKPGSSVKVSCKASFSWVRQAPGQGLEWMGSNYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCWGQGTLVTVSSAGGTFNSYAIIPIFGTTARYFDTYNNYGFAN", "metadata": {"pdb_id": "3ma9", "light_chain_seq": "IELTQPPSVSVVPGQTARISCSGDNIPYEYASWYQQKPGQAPVLVIYGDNNRPSGIPERFSGSNSGNTATLTISGTQAEDEADYYCASWDSMTVDGVFGGGTKLTVLGQ", "cdrh1_seq": "GGTFNSYA", "cdrh2_seq": "IIPIFGTT", "cdrh3_seq": "ARYFDTYNNYGFAN", "cdrl1_seq": "NIPYEY", "cdrl2_seq": "GDN", "cdrl3_seq": "ASWDSMTVDGV", "cdrh1_pos": "[23, 30]", "cdrh2_pos": "[48, 55]", "cdrh3_pos": "[94, 107]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 96]", "cdrh3_split": "val", "cdrh3_cluster": "4khx", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "Transmembrane glycoprotein (gp41), Human immunodeficiency virus 1", "target_domain": "N-heptad repeat (N-HR)", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing across a wide range of primary isolates from subtype B and C HIV-1"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 28961, 1020, 1010, 17, 18279, 13, 5133, 1920, 9117, 11424, 25618, 1927, 2616, 13141, 3413, 21, 18, 1920, 25618, 56, 17, 20662, 2015, 6865, 12, 56, 17, 3668, 13, 4952, 43, 29177, 17524, 17, 9121, 2409, 4324, 5289, 1930, 1977, 10551, 1966, 1925, 10974, 2758, 1958, 11984, 12130, 3788, 18, 1920, 3533, 1977, 4609, 1942, 25885, 3525, 17, 21, 2007, 7472, 1920, 3337, 1927, 1920, 3798, 17, 7864, 14142, 16, 8444, 9297, 1927, 1920, 5289, 2585, 16, 2743, 2651, 1920, 56, 17, 20662, 2015, 6865, 12, 56, 17, 3668, 13, 3031, 18, 1920, 3036, 3066, 8675, 5738, 16896, 9577, 1927, 1920, 56, 17, 3668, 20085, 16, 1956, 2353, 1942, 2559, 3533, 4206, 2743, 1942, 6582, 3402, 1990, 1920, 29177, 3154, 18, 3], "antigen": ["MQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAGHTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLEGQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLEGQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARIL"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A murine Fab (IGHV3/IGKV4-Kappa) targeting the Subtilisin-like protease 1 (PfSUB1) of Plasmodium falciparum. PfSUB1 is a serine protease that plays an essential role in merozoite invasion and egress from host erythrocytes by processing and activating various merozoite surface and parasitophorous vacuole proteins. The antibody is intended as a structural tool to facilitate crystallization of the protease-prodomain complex, binding within the Peptidase S8 domain on loop 1, which contains calcium-binding sites. What would the HCDRs be?", "target_protein": "QVQLQESGPDLVKPSSSLKLTCTTTWHWIRQEPGKSLEWMGYDYNDSLKARITITRDTASNMFFLQLSSVTSDDTAVYYCWGAGTTVTVSSAGYSISSGYSIHYSGSTVIYRYDGQWVFDD", "metadata": {"pdb_id": "4lvo", "light_chain_seq": "DIVLTQSPATMSASLGQRVSMSCSASSSVSTSYFHWYQQKPGSSPKLWIYSTSNLASGVPGRFSGSGSGTSYSLSISSMEAEDAATYYCHQFHRSPLTFGAGTKLELKRA", "cdrh1_seq": "GYSISSGYS", "cdrh2_seq": "IHYSGST", "cdrh3_seq": "VIYRYDGQWVFDD", "cdrl1_seq": "SSVSTSY", "cdrl2_seq": "STS", "cdrl3_seq": "HQFHRSPLT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "4lvo", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Subtilisin-like protease 1, Plasmodium falciparum", "target_domain": "Peptidase S8", "functional_role": "structural_tool", "evidence_quote": "monoclonal antibody Fab fragment required for successful crystallization"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 7135, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1920, 14745, 1921, 17, 3189, 7154, 21, 12, 11133, 2255, 1009, 13, 1927, 15663, 13098, 18, 11133, 2255, 1009, 1977, 43, 8468, 7154, 1988, 5705, 1925, 4415, 2770, 1922, 6902, 26553, 6254, 1930, 15850, 1979, 2037, 4423, 14161, 2007, 4587, 1930, 8019, 3425, 6902, 26553, 3154, 1930, 16891, 22575, 2080, 20309, 2697, 18, 1920, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 6628, 15416, 1927, 1920, 7154, 17, 21383, 2954, 1921, 2796, 16, 2743, 2651, 1920, 24050, 13808, 3418, 1990, 5881, 21, 16, 2154, 5461, 5016, 17, 2743, 3402, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["YHFNDEFRNLQWGLDLSRLDETQELINEHQVMSTRICVIDSGIDYNHPDLKDNIELNLKELHGRKGFDDDNNGIVDDIYGANFVNNSGNPMDDNYHGTHVSGIISAIGNNNIGVVGVDVNSKLIICKALDEHKLGRLGDMFKCLDYCISRNAHMINGSFSFDEYSGIFNSSVEYLQRKGILFFVSASNCSHPKSSTPDIRKCDLSINAKYPPILSTVYDNVISVANLKKNDNNNHYSLSINSFYSNKYCQLAAPGTNIYSTAPHNSYRKLNGTSMAAPHVAAIASLIFSINPDLSYKKVIQILKDSIVYLPSLKNMVAWAGYADINKAVNLAIKSK"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A human Fab, 110_C4 (IGHV1/IGLV10-Lambda), targeting an engineered Erythrocyte membrane protein 1 (PfEMP1) of Plasmodium falciparum. PfEMP1 is a parasite adhesin that mediates sequestration of infected erythrocytes in blood capillaries by binding endothelial cell receptors, driving severe malaria pathogenesis. The antibody is designed as a broadly neutralizing antibody that inhibits the PfEMP1\u2013EPCR interaction across CIDR\u03b11.4-8 variants, preventing parasite sequestration and severe disease. Please provide the HCDR sequences.", "target_protein": "QVHLVQSGAEVKKPGSSATVSCKASVSWVRQAPGQGLEWMGQTYAQRFQDRVTIRADETTSTIYMELNSLRSEDTAIYYCWGRGTTVTVSSGGPFRGYSIITMLDTIARNGNATVGSLGMDV", "metadata": {"pdb_id": "9naq", "light_chain_seq": "QAGLTQPPSESKGLRETATFTCTGNSNNVGNQGAAWLQQHQGHPPKLLSYRNNNRPSGISERFSASRSGNTASLTITGLQPEDEAVYFCSAWDTSLRAWLFGGGTHLTVLG", "cdrh1_seq": "GGPFRGYS", "cdrh2_seq": "IITMLDTI", "cdrh3_seq": "ARNGNATVGSLGMDV", "cdrl1_seq": "SNNVGNQG", "cdrl2_seq": "RNN", "cdrl3_seq": "SAWDTSLRAWL", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 99]", "cdrh3_split": "val", "cdrh3_cluster": "9naq", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "110_C4", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV10", "is_engineered": true, "target_antigen": "Erythrocyte membrane protein 1, Plasmodium falciparum", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "broadly inhibitory antibodies against severe malaria-associated PfEMP1 inhibiting the PfEMP1\u2013EPCR interaction"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 2616, 6914, 16, 8139, 41, 10872, 12, 20733, 7390, 19, 28961, 7390, 1008, 17, 18279, 13, 16, 5133, 1925, 11091, 15469, 3260, 2213, 21, 12, 5099, 19366, 1009, 13, 1927, 15663, 13098, 18, 5099, 19366, 1009, 1977, 43, 8652, 5315, 1921, 1988, 10412, 19001, 1927, 4014, 14161, 1922, 2877, 16973, 2007, 2743, 5003, 2024, 4086, 16, 9228, 4010, 7505, 6559, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1988, 7042, 1920, 5099, 19366, 1009, 229, 24464, 1005, 2835, 3436, 18069, 16806, 1009, 18, 24, 17, 28, 4936, 16, 8444, 8652, 19001, 1930, 4010, 2573, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["KFHNFFEMWVTYLLTETITWKDKLKTVCFDKWVKQKEDEWNSIKINIYFESFFFHVMKKLNKEAKWNKLMDAIELLLEYLKEKSTI"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the engineered Spike protein S1 of Pangolin coronavirus (GX/P2V/2017). The antibody is designed as a neutralizing antibody that maintains cross-reactive binding and neutralizing activity against the pangolin-origin coronavirus despite sequence variations in the RBD that cause most SARS-CoV-2 antibodies to lose binding. Please generate the HCDRs for this antibody.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7xsw", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[94, 113]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike protein S1, Pangolin coronavirus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "S309 maintained neutralizing activity with IC50 < 1 \u03bcg/mL against GX/P2V/2017 pseudovirus"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 2213, 4062, 1927, 3797, 3827, 7782, 5548, 10703, 12, 26615, 19, 7535, 1020, 19, 5664, 13, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 16566, 3567, 17, 6079, 2743, 1930, 12130, 2455, 3316, 1920, 3797, 3827, 7782, 17, 4853, 5548, 10703, 4281, 3244, 6740, 1922, 1920, 25780, 1988, 3936, 2501, 20466, 17, 6083, 17, 22, 3788, 1942, 15970, 2743, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["TNLCPFGEVFNASKFASVYAWNRKRISNCVADYSVLYNSTSFSTFKCYGVSPTKLNDLCFTNVYADSFVVKGDEVRQIAPGQTGVIADYNLPDDFTGCVIAWNSVKQDALTGGNYGYRLFRKSKLKPFERDIYQAGSTPCNGQVGLNCYYPLERYGFHPTTGVNYQPFRVVVLSFELLNGPATVCG"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human Fab, Fab25 (IGHV3/IGKV1-Kappa), targeting the Quinolone resistance protein NorA of Staphylococcus aureus. NorA is a membrane-associated active efflux pump that confers quinolone antibiotic resistance by extruding hydrophilic quinolones and lowering their intracellular concentration. The antibody is designed to inhibit NorA-mediated antibiotic efflux, thereby potentiating the efficacy of fluoroquinolone antibiotics against methicillin-resistant Staphylococcus aureus (MRSA) in combination therapy. Can you generate its HCDRs?", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVASSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVFNQGFTFSSSSISSSSGSTARWETGYYPYWRMYGFYWALDY", "metadata": {"pdb_id": "7lo7", "light_chain_seq": "IQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRT", "cdrh1_seq": "GFTFSSSS", "cdrh2_seq": "ISSSSGST", "cdrh3_seq": "ARWETGYYPYWRMYGFYWALDY", "cdrl1_seq": "QSVSSA", "cdrl2_seq": "SAS", "cdrl3_seq": "QQSSSSLIT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 117]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "7lo7", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Fab25", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Quinolone resistance protein NorA, Staphylococcus aureus", "target_domain": null, "functional_role": "other", "evidence_quote": "Fabs inhibit the quinolone transporter NorA; peptide mimics inhibit NorA and potentiate norfloxacin activity against MRSA"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 6914, 16, 6914, 4198, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 9012, 13048, 3554, 2213, 3990, 1019, 1927, 13452, 8849, 18, 3990, 1019, 1977, 43, 3260, 17, 2458, 3500, 11247, 8912, 1988, 16556, 9012, 13048, 7267, 3554, 2007, 2821, 9062, 14033, 9012, 24909, 1930, 11187, 2310, 4776, 3110, 18, 1920, 3533, 1977, 4609, 1942, 2875, 3990, 1019, 17, 3434, 7267, 11247, 16, 6113, 6849, 2287, 1920, 4348, 1927, 23619, 13048, 7560, 3316, 23025, 17, 4910, 13452, 8849, 12, 12836, 13, 1922, 3921, 3181, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["NKQIFVLYFNIFLIFLGIGLVIPVLPVYLKDLGLTGSDLGLLVAAFALSQMIISPFGGTLADKLIICIGLILFSVSEFMFAVGHNFSVLMLSRVIGGMSAGMVMPGVTGLIADISPSHQKAKNFGYMSAIINSGFILGPGIGGFMAEVSHRMPFYFAGALGILAFIMSIVLIHDPINWKVFITPVILTLVLSFGLSAFETLYSLYTADKVNYSPKDISIAITGGGIFGALFQIYFFDKFMKYFSELTFIAWSLLYSVVVLILLVFANDYWSIMLISFVVFIGFDMIRPAITNYFSNIAGERQGFAGGLNSTFTSMGNFIGPLIAGALFDVHIEAPIYMAIGVSLAGVVIVLIEKQHRAKL"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A human Fab (IGHV1/IGKV3-Kappa), X5, targeting the Envelope glycoprotein gp120 of Human immunodeficiency virus 1 in complex with the human CD4 receptor. The gp120 surface protein attaches the virus to the host lymphoid cell by binding to the primary receptor CD4, an interaction that induces structural rearrangement and creates a high-affinity binding site for chemokine coreceptors. This antibody forms a complex with gp120 and CD4, binding within the Third variable region (V3).", "target_protein": "LLEQSGAEVKKPGSSVQVSCKASFNWVRQAPGHGLEWMGGNYAQKFRGRVTFTADQATSTAYMELTNLRSDDTAVYYCWGQGTLVTVSSAGGTFSMYGIIPIFGTSARDFGPDWEDGDSYDGSGRGFFDF", "metadata": {"pdb_id": "2b4c", "light_chain_seq": "ELVLTQSPGTLSLSAGERATLSCRASQSVSSGSLAWYQQKPGQAPRLLIYGASTRATGIPDRFSGSGSGTDFTLTIGRLEPEDLAVYYCQQYGTSPYTFGQGTKLEIKRT", "cdrh1_seq": "GGTFSMYG", "cdrh2_seq": "IIPIFGTS", "cdrh3_seq": "ARDFGPDWEDGDSYDGSGRGFFDF", "cdrl1_seq": "QSVSSGS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYGTSPYT", "cdrh1_pos": "[23, 30]", "cdrh2_pos": "[48, 55]", "cdrh3_pos": "[94, 117]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "2b4c", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp120, Human immunodeficiency virus 1", "target_domain": "Third variable region (V3)", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 66, 1015, 16, 5133, 1920, 11262, 11424, 16102, 1927, 2616, 13141, 3413, 21, 1922, 2796, 1956, 1920, 2616, 4095, 3148, 18, 1920, 16102, 3154, 2213, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 1925, 2835, 1988, 6387, 4346, 14154, 1930, 15628, 43, 2149, 17, 5173, 2743, 3200, 1958, 11673, 30435, 3448, 18, 2052, 3533, 4952, 43, 2796, 1956, 16102, 1930, 4095, 16, 2743, 2651, 1920, 4563, 4650, 3031, 12, 14307, 13, 18, 3], "antigen": ["VVLENVTEHFNMWKNDMVEQMQEDIISLWDQSLKPCVKLTPLCVGAGSCDTSVITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESVEINCTRPNQNTRKSIHIGPGRAFYTTGEIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSAQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIE", "KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIV"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that engages the receptor-binding domain and recognizes a conserved glycan-containing epitope within the Sarbecovirus subgenus without competing with receptor attachment. Please output the HCDRs.", "target_protein": "VQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "6wps", "light_chain_seq": "IVLTQGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVE", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 114]", "cdrl1_pos": "[23, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 93]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 11580, 1036, 1920, 3148, 17, 2743, 3418, 1930, 16197, 43, 5305, 15060, 17, 3165, 10095, 2651, 1920, 9851, 12409, 7414, 22374, 1957, 2979, 11743, 1956, 3148, 8576, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLSLLIVNNATNVVIKVCEFQFCNDPFLGVNCTFEYVSFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKNYNYLYRKPFERDILQSYGFQPTNVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKSKRSFIEDLLFNKVTKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A human Fab, S9-3-37 (IGHV1/IGKV2-Kappa), targeting the Hemagglutinin of Influenza A virus (H5N1). Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for membrane fusion in the endosome. This antibody forms a complex with Hemagglutinin.", "target_protein": "QAQLVQSATEVKKPGASVKVSCQASFSWVRQAPGQGLEWMGWKFAEKFQDRVTMSIDTRTTTAYMEMRNLRFDDTAIYFCWGQGTTVIVSSAGFTFTSYGISAYDAKTAREFRTQIVLGYFDWLEGNAFDM", "metadata": {"pdb_id": "6e3h", "light_chain_seq": "DVVLTQTPLSSPVTRGQAASISCRSSQSLVHSDGNTYLSWIHQRPGQPPRLLIYKISKRFSGVPDRISGSGAGTEFTLTISRVEADDVGMYYCTQASQFPRTFGQGTKLEIKRT", "cdrh1_seq": "GFTFTSYG", "cdrh2_seq": "ISAYDAKT", "cdrh3_seq": "AREFRTQIVLGYFDWLEGNAFDM", "cdrl1_seq": "QSLVHSDGNTY", "cdrl2_seq": "KIS", "cdrl3_seq": "TQASQFPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 118]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "6e3h", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S9-3-37", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus (H5N1)", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 2616, 6914, 16, 16085, 17, 23, 17, 3191, 12, 20733, 7390, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 12, 20128, 13, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 3260, 5289, 1922, 1920, 22321, 18, 2052, 3533, 4952, 43, 2796, 1956, 26141, 18, 3], "antigen": ["GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISS", "GDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A human Fab, 2G7 (IGHV1/IGKV1-Kappa), targeting the Glutamate receptor ionotropic, NMDA 1 (GluN1) subunit of the N-methyl-D-aspartate receptor (NMDAR). GluN1 is a component of heterotetrameric, ligand-gated cation channels with high calcium permeability that participate in synaptic plasticity for learning and memory formation. The antibody is derived from a patient with autoimmune encephalitis and is designed to bind the N-terminal domain of GluN1, mediating receptor internalization and downregulation of synaptic NMDAR density and function.", "target_protein": "QVQLVQSGAEVRKPGASVKVSCRASVHWVRQAPGQGLEWLGWDYSQKFQGRVTMTRDTSITTAYVELSSLISDDTAVYYCWGQGTLVTVSSAGYSFTGYYINPNTGGTARDATGAASSPFDY", "metadata": {"pdb_id": "8jj2", "light_chain_seq": "DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQRPGQAPKLLIYMASTLQTGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHYKSYSFGPGTKVDIKR", "cdrh1_seq": "GYSFTGYY", "cdrh2_seq": "INPNTGGT", "cdrh3_seq": "ARDATGAASSPFDY", "cdrl1_seq": "QSISSW", "cdrl2_seq": "MAS", "cdrl3_seq": "QHYKSYS", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 94]", "cdrh3_split": "val", "cdrh3_cluster": "8jj2", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2G7", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Glutamate receptor ionotropic, NMDA 1, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "auto-mAbs induced the downregulation of synaptic NMDARs, without causing a tonic effect on channel activity, indicating that receptor internalization represents a major pathogenic mechanism"}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 16424, 1027, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 7627, 3148, 4755, 8405, 16, 10976, 21, 12, 19524, 1009, 13, 5903, 1927, 1920, 56, 17, 4963, 17, 46, 17, 12878, 3148, 12, 17585, 13, 18, 19524, 1009, 1977, 43, 4594, 1927, 19732, 28959, 17118, 16, 5207, 17, 12336, 9976, 5628, 1956, 2149, 5016, 8828, 1988, 7352, 1922, 6251, 8771, 1958, 4809, 1930, 4525, 3337, 18, 1920, 3533, 1977, 3595, 2037, 43, 2774, 1956, 8904, 18744, 1930, 1977, 4609, 1942, 4566, 1920, 56, 17, 4262, 3418, 1927, 19524, 1009, 16, 10239, 3148, 12071, 1930, 9894, 1927, 6251, 17585, 3824, 1930, 2347, 18, 3], "antigen": ["KIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSLSSAMWFSWGVLLNSGSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQNMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDAR"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A murine Fab, 7B11 (IGHV5/IGKV6-Kappa), targeting the engineered Envelope glycoprotein B of Suid alphaherpesvirus 1. This antibody forms a complex with the Envelope glycoprotein B, binding within the Herpesvirus glycoprotein B ectodomain C-terminal.", "target_protein": "EVQLVESGGGLVKPGGSLKLSCAASMSWVRQSPEKRLEWVATYYPDSVKGRFTISRDNAKNTLYLQMSSLRSDDTAIYYCWGQGTILTVSSAGFTFNDYAISGGGSYSTRQEGDFPLFDY", "metadata": {"pdb_id": "5zs0", "light_chain_seq": "DIVVTQSPKFMSTSAGDRVSITCKARQDVGSAVNWYQQKPGQSPKLLIYRASTRHTGVPDRFTGSGSGTDFTLTISSVQSEDVADYFCQQYGNYDLTFGAGTKLELKRA", "cdrh1_seq": "GFTFNDYA", "cdrh2_seq": "ISGGGSYS", "cdrh3_seq": "TRQEGDFPLFDY", "cdrl1_seq": "QDVGSA", "cdrl2_seq": "RAS", "cdrl3_seq": "QQYGNYDLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5zs0", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "7B11", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Envelope glycoprotein B, Suid alphaherpesvirus 1", "target_domain": "Herpesvirus glycoprotein B ectodomain C-terminal", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 11326, 3242, 12, 20733, 1020, 1015, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 11091, 11262, 11424, 44, 1927, 2020, 1960, 4595, 2380, 11860, 11074, 21, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 11262, 11424, 44, 16, 2743, 2651, 1920, 25718, 11424, 44, 27385, 45, 17, 4262, 18, 3], "antigen": ["RTAVRAAATERDRFYVCPPPSGSTVVRLEPEQACDMLSRIAAAWCELQNKDRTLWGEMSRLNPSAVATAALGQRVSARMLGDVMAISRCVEVRGGVYVQNSMRVPGERGTCYSRPLVTFEHNGTGVIEGQLGDDNELLISRDLIEPCTGNHRRYFKLGGGYVYYEDYSYVRMVEVPETISTRVTLNL"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, 3D2 (IGHV5/IGLV1-Lambda), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptor ACE2, initiating infection. The antibody is designed as a neutralizing antibody that binds to a conserved epitope within the Receptor-binding domain (RBD), conferring neutralizing activity against multiple SARS-CoV-2 variants including Beta, Alpha, Gamma, and Delta.", "target_protein": "EVQLVQSGAEVKKPGDSLKISCKGSIGWVRQKPGKGLEWMGIRYSPSSLGQVSISVDKSISTAYLQWSSLKASDTAMYYCWGQGTLVTVSSAGYSFANYWIYPGDSDTARHPIHGYGSGSLYNPDY", "metadata": {"pdb_id": "8bsf", "light_chain_seq": "SVLTQPPSVSAAPGQKVTISCSGSNSNIGINYVSWYQQLPETAPKLLIYENNQRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDTSLGAYVFGTGTKVTVLGQ", "cdrh1_seq": "GYSFANYW", "cdrh2_seq": "IYPGDSDT", "cdrh3_seq": "ARHPIHGYGSGSLYNPDY", "cdrl1_seq": "NSNIGINY", "cdrl2_seq": "ENN", "cdrl3_seq": "GTWDTSLGAYV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[24, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "8bsf", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "3D2", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "neutralized the interaction between the RBD and the cellular receptor angiotensin-converting enzyme 2 (ACE2) protein"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 5050, 1028, 12, 20733, 1020, 1015, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 3148, 8298, 1028, 16, 12410, 2909, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 6876, 1942, 43, 5305, 10095, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 21510, 12130, 2455, 3316, 3137, 20466, 17, 6083, 17, 22, 4936, 2710, 4666, 16, 4595, 16, 7034, 16, 1930, 9649, 18, 3], "antigen": ["CPFGEVFNATRFASVYAWNRKRISNCVADYSASFSTFKCYGVSPLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELVCG"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A human Fab, pertuzumab (IGHV3/IGKV1-Kappa), targeting an engineered variant of the Receptor tyrosine-protein kinase erbB-2 (HER2 S310F) of Homo sapiens. HER2 is a protein tyrosine kinase that regulates cell surface receptor signaling and transcriptional processes. The antibody is engineered with mutations (T30S/D31A) to overcome resistance conferred by the S310F mutation and is designed to mediate antigen-dependent cytotoxicity against HER2-expressing tumor cells.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASMDWVRQAPGKGLEWVADIYNQRFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTFSAYTVNPNSGGSARNLGPSFYFDY", "metadata": {"pdb_id": "9l1s", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCKASQDVSIGVAWYQQKPGKAPKLLIYSASYRYTGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYYIYPYTFGQGTKVEIKRT", "cdrh1_seq": "GFTFSAYT", "cdrh2_seq": "VNPNSGGS", "cdrh3_seq": "ARNLGPSFYFDY", "cdrl1_seq": "QDVSIG", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYYIYPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "1s78", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "pertuzumab", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Receptor tyrosine-protein kinase erbB-2 (HER2), Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "potent killing capacity through antigen-dependent cytotoxicity"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 2616, 6914, 16, 7548, 13535, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1925, 11091, 6031, 1927, 1920, 3148, 6941, 17, 2213, 4016, 11954, 17, 22, 12, 9162, 6080, 2930, 1038, 13, 1927, 16350, 27974, 18, 9162, 1977, 43, 2213, 6941, 4016, 1988, 7014, 2024, 3154, 3148, 3197, 1930, 5224, 4028, 18, 1920, 3533, 1977, 11091, 1956, 3527, 12, 9627, 1008, 1036, 19, 11319, 6146, 13, 1942, 9063, 3554, 16748, 2007, 1920, 6080, 2930, 1038, 3979, 1930, 1977, 4609, 1942, 8265, 4730, 17, 3100, 8470, 3316, 9162, 17, 4590, 2798, 2094, 18, 3], "antigen": ["TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDSPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGFCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRVLHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVA"]} {"modality_type": "antibody", "text": "What would be the HCDR sequences of an antibody with the following function: A human Fab, 506.C01 (IGHV4/IGKV1-Kappa), targeting the E2 glycoprotein of Chikungunya virus strain Senegal 37997. The E2 glycoprotein is part of the spike structure composed of trimers of E1-E2 heterodimers that mediate viral attachment and entry. The antibody is designed as a broadly neutralizing antibody against Chikungunya virus and related arthritogenic alphaviruses, targeting the apex of the B domain of the E2 glycoprotein.", "target_protein": "QVQLQESGPGLVKPSQTLSLTCTVSWTWIRLPPGKGLEWIGYYYNPSLKSRVTISLDRSKNQFSLKLSSVTAADTAVYFCWGQGTLVTVSSGGSISSDDYYIFYTGGTARAPETYCSTTNCYKGYFDS", "metadata": {"pdb_id": "8dwx", "light_chain_seq": "DIQMTQSPSSVSASVGDRVTITCRASQGISSWLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPRTFGQGTKVEIK", "cdrh1_seq": "GGSISSDDYY", "cdrh2_seq": "IFYTGGT", "cdrh3_seq": "ARAPETYCSTTNCYKGYFDS", "cdrl1_seq": "QGISSW", "cdrl2_seq": "AAS", "cdrl3_seq": "QQANSFPRT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 116]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8dwx", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "506.C01", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "E2 glycoprotein, Chikungunya virus strain Senegal 37997", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "potently neutralized CHIKV infection, and a subset inhibited multiple related arthritogenic alphaviruses"}}}, "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 29202, 18, 24948, 1009, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 6602, 11424, 1927, 7368, 1040, 3317, 1983, 9771, 3413, 3943, 6964, 11253, 1024, 28066, 8528, 18, 1920, 6602, 11424, 1977, 3131, 1927, 1920, 10429, 3170, 7179, 1927, 28220, 1927, 11123, 17, 6602, 21523, 1988, 8265, 4324, 8576, 1930, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 3316, 7368, 1040, 3317, 1983, 9771, 3413, 1930, 2712, 9273, 3027, 4575, 11216, 4595, 15506, 16, 5133, 1920, 14091, 1927, 1920, 44, 3418, 1927, 1920, 6602, 11424, 18, 3], "antigen": ["NFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHTCTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLMTQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMGQEPNYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQMSTNGTAHGHPHEIILYYYELYPTMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYELTPGATVPFLLSLLCCV"]} {"modality_type": "antibody", "text": "I want an antibody that has the function: A murine Fab, H6831 (IGHV1/IGKV11-Kappa), targeting the C-terminal region of Outer surface protein B of Borrelia burgdorferi. The antibody is designed as a bactericidal antibody capable of killing the pathogen in the absence of complement, targeting the C terminus of this major lipoprotein. Output the HCDRs.", "target_protein": "QVQLQQPGSVLVRPGASVKLSCKASMHWAKQRPGQGLEWIGEHYNEKFKGKATLTVDTSSSTAYVDLSSLTSEDSAVYYCWGQGTSVTVSSAGFTFTSSWIHPNSGNTARMRYGDYYAMDN", "metadata": {"pdb_id": "1rjl", "light_chain_seq": "DIQMNQSPSSLSASLGDTITITCHASQNINVWLNWFQQKPGSIPKLLIYMASNLHTGVPSRFSGSGSGTGFTLTISSLQPEDIATYYCQQGQSFPLTFGGGTKLEIKRA", "cdrh1_seq": "GFTFTSSW", "cdrh2_seq": "IHPNSGNT", "cdrh3_seq": "ARMRYGDYYAMDN", "cdrl1_seq": "QNINVW", "cdrl2_seq": "MAS", "cdrl3_seq": "QQGQSFPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "1rjl", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "H6831", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV11", "is_engineered": false, "target_antigen": "Outer surface protein B, Borrelia burgdorferi", "target_domain": null, "functional_role": "other", "evidence_quote": "bactericidal Fab fragments directed against the C terminus of outer surface protein B"}}}, "tokenized_instruction": [2, 51, 12914, 1925, 3533, 1988, 2258, 1920, 2347, 30, 43, 7135, 6914, 16, 26841, 11368, 1009, 12, 20733, 7390, 19, 7021, 1040, 7390, 1009, 17, 12093, 13, 16, 5133, 1920, 45, 17, 4262, 3031, 1927, 7642, 3154, 2213, 44, 1927, 27037, 2126, 24902, 18, 1920, 3533, 1977, 4609, 1966, 43, 20659, 3533, 7131, 1927, 11879, 1920, 7055, 1922, 1920, 3905, 1927, 5508, 16, 5133, 1920, 45, 7822, 1927, 2052, 3044, 9694, 18, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["TVEIKEGTVTLKREIEKDGKVKVFLNDTAGSNKKTGKWEDSTSTLTISADSKKTKDLVFLTDGTITVQQYNTAGTSLEGSASEIKNLSELKNALK"]} {"modality_type": "antibody", "text": "I want an antibody that has the function: A human Fab, 356 (IGHV3/IGKV3-Kappa), targeting the Circumsporozoite protein of Plasmodium falciparum. The Circumsporozoite protein is an essential sporozoite protein required for sporozoite migration through the host dermis and infection of host hepatocytes, and binds to highly sulfated heparan sulfate proteoglycans on the surface of host hepatocytes. The antibody is designed as a neutralizing antibody that engages the NPNA repeat epitope with high avidity through multivalent binding and homotypic Fab-Fab interactions to confer protection against malaria infection. Output the HCDRs.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQTPGKGLEWVAVFYADSVEGRFTISRDNSKNMIYLQMNSLRVEDTAIYYCWGQGTLVTVSSGFTFRNFGIWHDGSNKARDSLFYDHDNSGYYGY", "metadata": {"pdb_id": "8dz4", "light_chain_seq": "QIVMTQSPATVSVSPGERATLSCRASRSVTSKLAWYQQKPGQAPRLLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAVYFCQQYNNGFTFGPGTKVDFK", "cdrh1_seq": "GFTFRNFG", "cdrh2_seq": "IWHDGSNK", "cdrh3_seq": "ARDSLFYDHDNSGYYGY", "cdrl1_seq": "RSVTSK", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYNNGFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6w05", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "356", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Circumsporozoite protein, Plasmodium falciparum", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "demonstrate in vivo protection in a liver burden assay"}}}, "tokenized_instruction": [2, 51, 12914, 1925, 3533, 1988, 2258, 1920, 2347, 30, 43, 2616, 6914, 16, 27069, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 28868, 2074, 26553, 2213, 1927, 15663, 13098, 18, 1920, 28868, 2074, 26553, 2213, 1977, 1925, 4415, 9130, 26553, 2213, 3414, 1958, 9130, 26553, 5049, 2596, 1920, 4423, 20201, 1930, 2909, 1927, 4423, 9919, 16, 1930, 6876, 1942, 3626, 26649, 22024, 8767, 25185, 1990, 1920, 3154, 1927, 4423, 9919, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 11580, 1036, 1920, 5007, 2175, 6865, 10095, 1956, 2149, 24673, 2596, 5738, 16896, 2743, 1930, 16350, 5518, 1935, 6914, 17, 6914, 3719, 1942, 7909, 6202, 3316, 7505, 2909, 18, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["DPNANPNVDPNANPNVDPNANPNVDPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNA"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A murine Fab, 2D3 (IGHV2/IGKV1-Kappa), targeting the prefusion Fusion glycoprotein F0 of Nipah henipavirus. The Fusion glycoprotein F0 is a class I viral fusion protein that directs fusion of viral and cellular membranes, leading to delivery of the nucleocapsid into the cytoplasm. The antibody is designed as a neutralizing antibody against the prefusion conformation of NiV F, binding to a quaternary apical epitope on domain 3. What would the HCDRs be?", "target_protein": "QVQLKQSGPGLVAPSQSLSITCTVSLSWVRQPPGKGLEWLGVNYNSALKSRLTISKDNSKSQVFLKMNSLQSEDTARYYCWGQGTSVTVSAGFSLTSYAIWVGGVTASRHLSTGAMDY", "metadata": {"pdb_id": "7up9", "light_chain_seq": "DVLMTQSPLSLPVSLGDQASISCRSSQSIVHSNGDTYFEWYLQKPGQSPKLLIYKVSNRFSGVPNRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSYVPYTFGGGTKLEIK", "cdrh1_seq": "GFSLTSYA", "cdrh2_seq": "IWVGGVT", "cdrh3_seq": "ASRHLSTGAMDY", "cdrl1_seq": "QSIVHSNGDTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQGSYVPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 106]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "7up9", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2D3", "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Fusion glycoprotein F0, Nipah henipavirus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "ten neutralizing antibodies against NiV prefusion F"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 7135, 6914, 16, 24443, 12, 20733, 15755, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 9328, 2670, 5289, 11424, 17930, 1927, 18786, 5945, 14618, 19514, 11074, 18, 1920, 5289, 11424, 17930, 1977, 43, 2921, 51, 4324, 5289, 2213, 1988, 28351, 5289, 1927, 4324, 1930, 3689, 5726, 16, 4523, 1942, 4868, 1927, 1920, 2797, 28712, 1960, 2460, 1920, 5239, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 3316, 1920, 9328, 2670, 7748, 1927, 18054, 48, 16, 2743, 1942, 43, 21920, 8913, 10095, 1990, 3418, 23, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["ILHYEKLSKIGLVKGVTRKYKIKSNPLTKDIVIKMIPNVSNMSQCTGSVMENYKTRLNGILTPIKGALEIYKNNTHDCGVCMAGVAIGIATAAQITAGVALYEAMKNADNINKLKSSIESTNEAVVKLQETAEKTVYVFTALQDYINTNLVPTIDKIPCKQTELSLDLALSKYLSDLLFVFGPNLQDPVSNSMTIQAISQAFGGNYETLLRTLGYATEDFDDLLESDSITGQIIYVDLSSYYIIVRVYFPILTEIQQAYIQELLPVSFNNDNSEWISIVPNFILVRNTLISNIEIGFCLITKRSVICNQDYATPMTNNMRECLTGSTEKCPRELVVSSHVPRFALSNGVLFANCISVTCQCQTTGRAISQSGEQTLLMIDNTTCPTAVLGNVIISLGKYLGSVNYNSEGIAIGPPVFTDKVDISSQISSMNQSLQQSKDYIK"]} {"modality_type": "antibody", "text": "I want an antibody that has the function: A human Fab, 2-15 (IGHV1/IGLV2-Lambda), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the host cell membrane by interacting with ACE2 receptor and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting the receptor-binding domain (RBD), which overlaps the ACE2 binding site, and is part of the prevalent VH1-2 antibody class that recognizes the RBD with convergent heavy- and light-chain modules. Output the HCDRs.", "target_protein": "VQLVQSGAEVKKPGASVRVSCKASMHWVRQAPGQGLEWMGWNYAQKFQGWVTMTRDTSISTVYMELSRLRSDDTAVYYCWGQGTMITVGYTFTGYYINPISDGTARGGSRCSGGNCYGWAYDAFDI", "metadata": {"pdb_id": "7l57", "light_chain_seq": "SALTQPASVSGSPGQSITISCTGTSSDVGGYNFVSWYQQHPGKAPKLMIYDVSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADCYCSSYTSSSTFVFGTGTKVTVLG", "cdrh1_seq": "GYTFTGYY", "cdrh2_seq": "INPISDGT", "cdrh3_seq": "ARGGSRCSGGNCYGWAYDAFDI", "cdrl1_seq": "SSDVGGYNF", "cdrl2_seq": "DVS", "cdrl3_seq": "SSYTSSSTFV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 116]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "7l5b", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2-15", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV2", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "2-15 nAbs neutralize authentic SARS-CoV-2 live virus with an IC50 of 0.0007 \u03bcg/mL"}}}, "tokenized_instruction": [2, 51, 12914, 1925, 3533, 1988, 2258, 1920, 2347, 30, 43, 2616, 6914, 16, 22, 17, 2461, 12, 20733, 7390, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 2154, 19853, 1920, 8298, 1028, 2743, 3200, 16, 1930, 1977, 3131, 1927, 1920, 8942, 14693, 1009, 17, 22, 3533, 2921, 1988, 16197, 1920, 25780, 1956, 18489, 7881, 17, 1930, 3696, 17, 4659, 10803, 18, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["YTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLFRVYSSANNCTFEYVSKNLREFVFKNIDGYFKIYSKHTPIDLPQGFSALEPLVDLPIITRFQTLLAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVLYNSASFSTFKCYGVCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPE"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (Omicron variant B.1.1.529). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a broadly neutralizing antibody against sarbecovirus spike proteins. Please generate its HCDRs.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7tly", "light_chain_seq": "IVLTQSPGTLPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVE", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[22, 28]", "cdrl2_pos": "[46, 48]", "cdrl3_pos": "[85, 92]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 7254, 1935, 2830, 6031, 44, 18, 21, 18, 21, 18, 4764, 1026, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 3316, 9851, 12409, 7414, 10429, 2697, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["ITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGP"]} {"modality_type": "antibody", "text": "A human Fab, PGZL1 (IGHV1/IGKV3-Kappa), targeting the membrane-proximal external region (MPER) of the Envelope glycoprotein gp160 of Human immunodeficiency virus 1. The Envelope glycoprotein gp160 oligomerizes into trimers and mediates viral attachment to host cells and membrane fusion. The antibody is designed as a broadly neutralizing antibody targeting the MPER epitope on the viral membrane, with a 15-residue CDRH3 and reduced polyreactivity compared to other MPER-targeting bnAbs. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "QVQLVQSGAEVKKPGSSVKVSCKASISWVRQAPGQGLEWMGGNYAQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCWGQGTVITVSSAGGTFSSYAIIPIFGTAAREGEGWFGKPLRAFEF", "metadata": {"pdb_id": "6o42", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGTSQSTFGQGTRLEIKRT", "cdrh1_seq": "GGTFSSYA", "cdrh2_seq": "IIPIFGTA", "cdrh3_seq": "AREGEGWFGKPLRAFEF", "cdrl1_seq": "QSVSSSY", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYGTSQST", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "6mto", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "PGZL1", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus 1", "target_domain": "MPER", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibody from an HIV-infected person that recognizes the membrane-proximal external region (MPER)"}}}, "tokenized_instruction": [2, 43, 2616, 6914, 16, 5306, 26262, 1009, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 1927, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 21, 18, 1920, 11262, 11424, 4882, 16954, 13034, 4517, 2460, 28220, 1930, 10412, 4324, 8576, 1942, 4423, 2094, 1930, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 5438, 1915, 10095, 1990, 1920, 4324, 3260, 16, 1956, 43, 2461, 17, 6181, 20170, 18649, 1930, 3028, 4286, 1936, 5454, 2452, 1942, 2303, 5438, 1915, 17, 5133, 11006, 8805, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["NWFDITNWLWYIKKK"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A rhesus macaque Fab, NCI05 (IGHV3/IGLV1-Lambda), targeting the SIV V2 peptide derived from the Envelope glycoprotein gp160 of Simian immunodeficiency virus. The surface protein gp120 attaches the virus to host lymphoid cells by binding the primary receptor CD4, inducing structural rearrangement that creates a high-affinity binding site for chemokine coreceptors, and also targets the virus to gut-associated lymphoid tissue via integrin binding. The antibody is designed to target a transient, partially opened state of the viral spike apex within the Variable region 2 (V2), with mucosal levels correlating with delayed SIV acquisition.", "target_protein": "EVQLVESGGGLAKPGGSLRLSCAASIHWVRQAPGKGLEWVSVYYADSVEGRFTISRDNSKNTLSLQMNSLRTEDTAVYYCWGQGVLVTVSSAGFTFSRYAISSGGSTAKDATPYYYSGGYWYVGNYSFDY", "metadata": {"pdb_id": "8fbw", "light_chain_seq": "QSVLTQPPSASGAPGQSVTISCSGSSSNIGSNYVYWYQQLSGKAPKLLIYNNNQRPSGVPDRFSGSKSGTSASLAISGLQSKDEADYYCSAWDSSLNDPLFGGGTRLTVLGQ", "cdrh1_seq": "GFTFSRYA", "cdrh2_seq": "ISSGGST", "cdrh3_seq": "AKDATPYYYSGGYWYVGNYSFDY", "cdrl1_seq": "SSNIGSNY", "cdrl2_seq": "NNN", "cdrl3_seq": "SAWDSSLNDPL", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 117]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 99]", "cdrh3_split": "val", "cdrh3_cluster": "8fbw", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "NCI05", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "SIV V2 peptide, Simian immunodeficiency virus", "target_domain": "Variable region 2 (V2)", "functional_role": "other", "evidence_quote": "NCI05 delays SIV mac251 acquisition; mucosal levels strongly correlated with delayed acquisition"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 16996, 20533, 6914, 16, 14188, 15264, 12, 20733, 1020, 1010, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 14398, 12701, 4207, 3595, 2037, 1920, 11262, 11424, 4882, 16954, 1927, 30130, 13141, 3413, 18, 1920, 3154, 2213, 16102, 5823, 1918, 1920, 3413, 1942, 4423, 11751, 2094, 2007, 2743, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1988, 15628, 43, 2149, 17, 5173, 2743, 3200, 1958, 11673, 30435, 3448, 16, 1930, 2222, 4845, 1920, 3413, 1942, 7660, 17, 2458, 11751, 2960, 3454, 8920, 2743, 18, 1920, 3533, 1977, 4609, 1942, 2758, 43, 6809, 16, 6426, 16645, 3360, 1927, 1920, 4324, 10429, 14091, 2651, 1920, 4650, 3031, 22, 12, 12701, 13, 16, 1956, 9565, 2428, 20117, 1956, 7083, 14398, 6165, 18, 3], "antigen": ["LKSDKKIEYNETWYSR"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A human Fab, 218 (IGHV3), targeting the engineered Ig-like V-type domain of human Tyrosine-protein phosphatase non-receptor type substrate 1 (Signal regulatory protein alpha). This receptor acts as an immunoglobulin-like cell surface receptor for CD47 and mediates negative regulation of phagocytosis and immune cell activation. The antibody is designed as a non-blocking anti-SIRP\u03b1 antibody that enhances macrophage-mediated antibody-dependent cellular phagocytosis of tumor cells through SIRP\u03b1 engagement independent of CD47 blockade.", "target_protein": "DVQLVESGGGVVRPGESLTLSCTASMNWVRQAPGEGLDWVSSYYADSVKGRATISRDNSKNTLYLRLFSLRADDTAIYYCWGPGTLVTVSSAGFTFTSSTISTSGVITATDTFDH", "metadata": {"pdb_id": "6nmv", "light_chain_seq": "ALTQPASVSANPGETVKITCFGSSGNYGWFQQKSPGSAPVTVIHYNNKRPSDIPSRFSGSKSGSTGTLTITGVRAEDEAVYFCGAWETGSATFGAGTTLTVLGQ", "cdrh1_seq": "GFTFTSST", "cdrh2_seq": "ISTSGVIT", "cdrh3_seq": "ATDTFDH", "cdrl1_seq": "SGNYG", "cdrl2_seq": "YNN", "cdrl3_seq": "GAWETGSAT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 102]", "cdrl1_pos": "[23, 27]", "cdrl2_pos": "[44, 46]", "cdrl3_pos": "[83, 91]", "cdrh3_split": "val", "cdrh3_cluster": "6nmv", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "218", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "unknown", "is_engineered": true, "target_antigen": "Tyrosine-protein phosphatase non-receptor type substrate 1 (Signal regulatory protein alpha), Homo sapiens", "target_domain": "Ig-like V-type", "functional_role": "other", "evidence_quote": "non-blocking anti-SIRP\u03b1 antibodies also enhance macrophage phagocytosis"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 17810, 12, 20733, 1020, 1010, 13, 16, 5133, 1920, 11091, 7021, 17, 3189, 64, 17, 2601, 3418, 1927, 2616, 6941, 17, 2213, 8167, 2447, 17, 3148, 2601, 4510, 21, 12, 2733, 4948, 2213, 4595, 13, 18, 2052, 3148, 8016, 1966, 1925, 11837, 17, 3189, 2024, 3154, 3148, 1958, 29741, 1930, 10412, 3136, 3640, 1927, 13715, 1930, 3743, 2024, 2936, 18, 1920, 3533, 1977, 4609, 1966, 43, 2447, 17, 7472, 2246, 17, 4520, 1034, 1071, 3533, 1988, 9515, 8088, 17, 3434, 3533, 17, 3100, 3689, 13715, 1927, 2798, 2094, 2596, 4520, 1034, 1071, 9577, 3484, 1927, 29741, 9847, 18, 3], "antigen": ["ELQVIQPDKSVLVAAGETATLRCTATSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRIGAITPADAGTYYCVKFRKGSPDDVEFKSGAGTELSVRAKP"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A murine Fab, 7C11 (IGHV14/IGKV6-Kappa), targeting the Aspartic protease Bla g 2 of the German cockroach (Blattella germanica). Bla g 2 functions as a digestive enzyme in the cockroach and is a major allergen that induces mast cell degranulation. The antibody is designed to recognize the IgE-binding epitope on Bla g 2, binding within the Peptidase A1 domain, to provide guidance for allergen-specific immunotherapy vaccine development.", "target_protein": "EIQLQQSGAELVKPGASVKLSCTASIHWVKQRPEQGLEWIGRRYGPKFLGKATITADTSSNTAYLHLNSLTSEDTAVYFCWGQGTSVTVSSAGFNIKDTYIDPANGNTARWVRQMDY", "metadata": {"pdb_id": "2nr6", "light_chain_seq": "DIVMTQSHKFMSTSVGDRVSITCKASQIVSTAVAWYQQKPGQSPKLLIYSASYRYTGVPDRFTGSGSGTDFTFTISSVQAEDLAVYYCQQHYNSPQTFGGGTKLEIKRA", "cdrh1_seq": "GFNIKDTY", "cdrh2_seq": "IDPANGNT", "cdrh3_seq": "ARWVRQMDY", "cdrl1_seq": "QIVSTA", "cdrl2_seq": "SAS", "cdrl3_seq": "QQHYNSPQT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 104]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "2nr6", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "7C11", "antibody_format": "Fab", "heavy_subclass": "IGHV14", "light_subclass": "IGKV6", "is_engineered": false, "target_antigen": "Aspartic protease Bla g 2, Blattella germanica", "target_domain": "Peptidase A1", "functional_role": "other", "evidence_quote": "7C11 shares a binding epitope with IgE; guidance for immunotherapy vaccine design"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 7135, 6914, 16, 13733, 3242, 12, 20733, 7390, 1006, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 23047, 7154, 18208, 49, 22, 1927, 1920, 12194, 11379, 1931, 2155, 12, 18208, 3519, 5870, 12194, 6102, 13, 18, 18208, 49, 22, 4088, 1966, 43, 15486, 4113, 1922, 1920, 11379, 1931, 2155, 1930, 1977, 43, 3044, 15468, 1988, 6387, 9731, 2024, 23712, 18, 1920, 3533, 1977, 4609, 1942, 9967, 1920, 10777, 17, 2743, 10095, 1990, 18208, 49, 22, 16, 2743, 2651, 1920, 24050, 8080, 3418, 16, 1942, 3394, 9765, 1958, 15468, 17, 2487, 12748, 5955, 2740, 18, 3], "antigen": ["GASIVPLYKLVHVFINTQYAGITKIGNQNFLTVFDSTSCNVVVASQECVGGACVCPNLQKYEKLKPKYISDGNVQVKFFDTGSAVGRGIEDSLTISQLTTSQQDIVLADELSQEVCILSADVVVGIAAPGCPNALKGKTVLENFVEENLIAPVFSIHHARFQDGEHFGEIIFGGSDWKYVDGEFTYVPLVGDDSWKFRLDGVKIGDTTVAPAGTQAIIDTSKAIIVGPKAYVNPINEAIGCVVEKTTTRRICKLDCSKIPSLPDVTFVINGRNFNISSQYYIQQNGNLCYSGFQPGHSDHFFIGDFFVDHYYSEFNWENKTMGFGRSVE"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A murine Fab (IGHV5/IGKV8-Kappa) targeting the e-antigen of Hepatitis B virus. The e-antigen is a non-particulate variant of the capsid protein that may regulate immune response to the intracellular capsid by acting as a T-cell tolerogen and preventing destruction of infected cells by cytotoxic T-cells. This antibody forms a complex with the e-antigen dimer. Please generate its HCDRs.", "target_protein": "EVQLVESGGDLVKPGGSLKLSCAASMSWVRQTPDKRLEWVATYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCWGQGTSVTVSSAGFTFSSYGISSGGNYITREGAYSGSSSYPMDY", "metadata": {"pdb_id": "3v6z", "light_chain_seq": "NIMMTQSPSSLAVSAGEKVTMNCKSSQSVLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQTEDLAVYYCHQYLSSYMYTFGGGTKLEIKRA", "cdrh1_seq": "GFTFSSYG", "cdrh2_seq": "ISSGGNYI", "cdrh3_seq": "TREGAYSGSSSYPMDY", "cdrl1_seq": "QSVLYSSNQKNY", "cdrl2_seq": "WAS", "cdrl3_seq": "HQYLSSYMYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 103]", "cdrh3_split": "val", "cdrh3_cluster": "3v6z", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV8", "is_engineered": false, "target_antigen": "e-antigen, Hepatitis B virus", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 1020, 1015, 19, 7021, 1040, 1020, 1025, 17, 12093, 13, 5133, 1920, 47, 17, 4730, 1927, 7977, 44, 3413, 18, 1920, 47, 17, 4730, 1977, 43, 2447, 17, 17766, 6031, 1927, 1920, 14681, 2213, 1988, 2278, 5741, 3743, 2644, 1942, 1920, 4776, 14681, 2007, 8290, 1966, 43, 62, 17, 2024, 4977, 2404, 1930, 8444, 12102, 1927, 4014, 2094, 2007, 8377, 62, 17, 2094, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 47, 17, 4730, 7632, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["CLGWLWGMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISALTFGRETVLEYLVSFAVWIRTPPAYRPPNAPILS"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A human Fab, ZK2B10 (IGHV1/IGLV1-Lambda), targeting the Genome polyprotein of Zika virus. The Genome polyprotein includes the envelope glycoprotein, which mediates viral entry and membrane fusion. The antibody is designed as a neutralizing antibody that prevents membrane fusion by blocking steps between the formation of the fusion intermediate and membrane merger, binding within Domain III (DIII).", "target_protein": "EVQLVQSGAEVKKPGASVKVSCKASINWVRQATGQGLEWMGWGYAQKFQGRVTMTRNTSINTAYMELSSLRSEDTAVYYCWGQGTTVTVSSAGYTFTSGHTFPSYDMNPNRGNTARVRSGTNYGSYYYYYYGMDV", "metadata": {"pdb_id": "6jep", "light_chain_seq": "SYELTQPPSASGTPGQRVTISCSGSSSNIGNNYVHWYQQLPGSAPKLLIYRNNQRPSGVPDRFSGSKSGTSGSLAISGLRSEDEADYYCASWDDSLSGHWVFGGGTKVTVLGQ", "cdrh1_seq": "GYTFTSGHTFPSYD", "cdrh2_seq": "MNPNRGNT", "cdrh3_seq": "ARVRSGTNYGSYYYYYYGMDV", "cdrl1_seq": "SSNIGNNY", "cdrl2_seq": "RNN", "cdrl3_seq": "ASWDDSLSGHWV", "cdrh1_pos": "[25, 38]", "cdrh2_pos": "[56, 63]", "cdrh3_pos": "[102, 122]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 100]", "cdrh3_split": "val", "cdrh3_cluster": "6jfi", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ZK2B10", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "Genome polyprotein, Zika virus", "target_domain": "Domain III (DIII)", "functional_role": "neutralizing", "evidence_quote": "capable of protection against Zika virus infection; functions at steps between fusion intermediate and membrane fusion"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 68, 6779, 5090, 1008, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 3843, 6240, 5684, 1927, 28593, 3413, 18, 1920, 3843, 6240, 5684, 5921, 1920, 11262, 11424, 16, 2154, 10412, 4324, 6904, 1930, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 10299, 3260, 5289, 2007, 7472, 5983, 2192, 1920, 3337, 1927, 1920, 5289, 6129, 1930, 3260, 27399, 1005, 16, 2743, 2651, 3418, 4337, 12, 26028, 1033, 13, 18, 3], "antigen": ["VSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRS"]} {"modality_type": "antibody", "text": "Here is the antibody function: A murine Fab (IGHV1/IGKV4-Kappa) targeting the engineered T-cell surface glycoprotein CD4 of Homo sapiens. CD4 serves as the primary receptor for human immunodeficiency virus-1 (HIV-1) and plays an essential role in immune responses as a coreceptor for MHC class II molecule:peptide complexes. The antibody is designed as a neutralizing antibody that blocks HIV-1 infection by targeting an epitope in the second domain of CD4 without interfering with immune functions mediated by CD4 interaction with MHC class II molecules. Generate the corresponding HCDRs.", "target_protein": "QVQLQQSGPEVVKPGASVKMSCKASIHWVRQKPGQGLDWIGYDYDEKFKGKATLTSDTSTSTAYMELSSLRSEDTAVYYCWGQGTLVTVSSAGYTFTSYVINPYNDGTAREKDNYATGAWFAY", "metadata": {"pdb_id": "3o2d", "light_chain_seq": "DIVMTQSPDSLAVSLGERVTMNCKSSQSLLYSTNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSVQAEDVAVYYCQQYYSYRTFGGGTKLEIKRT", "cdrh1_seq": "GYTFTSYV", "cdrh2_seq": "INPYNDGT", "cdrh3_seq": "AREKDNYATGAWFAY", "cdrl1_seq": "QSLLYSTNQKNY", "cdrl2_seq": "WAS", "cdrl3_seq": "QQYYSYRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 101]", "cdrh3_split": "val", "cdrh3_cluster": "7t0r", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": true, "target_antigen": "T-cell surface glycoprotein CD4, Homo sapiens", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "potently blocks HIV-1 infection and targets an epitope in the second domain of CD4"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1920, 11091, 62, 17, 2024, 3154, 11424, 4095, 1927, 16350, 27974, 18, 4095, 10634, 1966, 1920, 3065, 3148, 1958, 2616, 13141, 3413, 17, 21, 12, 3525, 17, 21, 13, 1930, 5705, 1925, 4415, 2770, 1922, 3743, 3387, 1966, 43, 30435, 2684, 1958, 8709, 2921, 2890, 5388, 30, 4207, 5048, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 3525, 17, 21, 2909, 2007, 5133, 1925, 10095, 1922, 1920, 2812, 3418, 1927, 4095, 2979, 13369, 1956, 3743, 4088, 3434, 2007, 4095, 2835, 1956, 8709, 2921, 2890, 4206, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLA"]} {"modality_type": "antibody", "text": "I want an antibody that has the function: A human Fab, 4E10 (IGHV1/IGKV3-Kappa), targeting the Envelope glycoprotein gp41 of Human immunodeficiency virus 1. The gp41 protein mediates fusion of viral and host cell membranes during entry and is proteolytically cleaved from the gp160 precursor. The antibody is designed as a neutralizing antibody targeting the MPER epitope, which forms a composite epitope with viral membrane lipids including phosphatidic acid and phosphatidylglycerol that are transiently exposed during HIV infection and budding. Output the HCDRs.", "target_protein": "QVQLVQSGAEVKRPGSSVTVSCKASLSWVRQAPGRGLEWMGGNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCWGQGTLVTVSSAGGSFSTYAVIPLLTITAREGTTLGKPIGAFAH", "metadata": {"pdb_id": "4xbe", "light_chain_seq": "EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRT", "cdrh1_seq": "GGSFSTYA", "cdrh2_seq": "VIPLLTIT", "cdrh3_seq": "AREGTTLGKPIGAFAH", "cdrl1_seq": "QSVGNNK", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYGQSLST", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "5x08", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "4E10", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160 (gp41), Human immunodeficiency virus 1", "target_domain": "MPER", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody responses against the highly conserved MPER region"}}}, "tokenized_instruction": [2, 51, 12914, 1925, 3533, 1988, 2258, 1920, 2347, 30, 43, 2616, 6914, 16, 10800, 2930, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 25618, 1927, 2616, 13141, 3413, 21, 18, 1920, 25618, 2213, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 1930, 1977, 12712, 2169, 10246, 2037, 1920, 4882, 16954, 7897, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 5438, 1915, 10095, 16, 2154, 4952, 43, 7895, 10095, 1956, 4324, 3260, 8238, 2710, 2766, 8525, 1935, 2687, 1930, 10951, 18207, 1988, 2032, 12145, 4616, 2409, 3525, 2909, 1930, 15909, 18, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["NWFDITNWLWYIKKK"]} {"modality_type": "antibody", "text": "Here is the antibody function: A murine Fab (IGHV1/IGKV8-Kappa) targeting the Growth hormone secretagogue receptor type 1 (ghrelin receptor) of Homo sapiens. The ghrelin receptor is a G protein-coupled receptor specific to ghrelin, an appetite-regulating peptide hormone, and upon activation stimulates appetite and promotes growth hormone secretion. This antibody is intended as a structural tool to stabilize the intracellular loop 3 (ICL3) and facilitate crystallization of the ghrelin receptor. Generate the corresponding HCDRs.", "target_protein": "EVQLQQSGAELVRPGASVKLSCKASMHWVKQTPVHGLEWIGAVYNQKFKGKATLTADISSTTAYMELRSLTSEDSAVYFCWGQGTTLTVSSAGYTFTDYEIDPETGGTISEDIDESKDY", "metadata": {"pdb_id": "6ko5", "light_chain_seq": "DIVMTQSPSSLAVSAGEKVTLSCKSSQSLFNSRTRKNYLAWYQQKPGLSPTLLIYWASTRKSGVPDRFTGSGSGTDFTLTITSVQAEDLAVYYCKQSYYLRTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTDYE", "cdrh2_seq": "IDPETGGT", "cdrh3_seq": "ISEDIDESKDY", "cdrl1_seq": "QSLFNSRTRKNY", "cdrl2_seq": "WAS", "cdrl3_seq": "KQSYYLRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 101]", "cdrh3_split": "val", "cdrh3_cluster": "6ko5", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV8", "is_engineered": false, "target_antigen": "Growth hormone secretagogue receptor type 1, Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "Fab 7881 stabilizes ICL3 and improves thermostability of the ghrelin receptor, allowing it to form crystals"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1025, 17, 12093, 13, 5133, 1920, 2905, 6365, 8571, 28294, 2182, 3148, 2601, 21, 12, 16703, 3148, 13, 1927, 16350, 27974, 18, 1920, 16703, 3148, 1977, 43, 49, 2213, 17, 6416, 3148, 2487, 1942, 16703, 16, 1925, 17990, 17, 6773, 4207, 6365, 16, 1930, 4073, 2936, 11803, 17990, 1930, 7383, 2905, 6365, 5512, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 1920, 4776, 5881, 23, 12, 25175, 1010, 13, 1930, 6628, 15416, 1927, 1920, 16703, 3148, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["DLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLPAPLLAGVTATCVALFVVGIAGNLLTMLVVSRFRELRTTTNLYLSSMAFSDLLIFLCMPLDLVRLWQYRPWNFGDLLCKLFQFVSESCTYAKVLTITALSVERYFAICFPLRAKVVVTKGRVKLVIFVIWAVAFCSAGPIFVLVGVEHEQGTDPWDTNECRPTEFAVRSGLLTVMVWVSSIFFFLPVFCLTVLYSLIGRKLWRRRRGDAVVGASLRDQNHKQTVKMLAVVVFAFILCWLPFHVGRYLFSKSFEPSQYCNLVSFVLFYLSAAINPILYNIMSKKYRVAVFRLLG"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A human Fab, 2530 (IGHV4/IGKV1-Kappa), targeting the engineered 25 kDa ookinete surface antigen (Pfs25) of Plasmodium falciparum. Pfs25 is displayed on the ookinete surface during the parasite's development in the mosquito midgut. The antibody is designed as a transmission-blocking antibody that inhibits parasite development in the mosquito vector, binding to a novel epitope (Site 3) on the Pfs25 EGF2 domain.", "target_protein": "QVQLQESGPGLVKPSETLSLTCTVSWSWIRQPAGKGLEWIGRNYNPSLKSRVTMSVDTSNNHFSMRLNSVTAADTAVYYCWGQGTLVTVSSAGDSMSSYYISTSGSTACSGSYSFFDY", "metadata": {"pdb_id": "6phb", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCQASQDISNFLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLRIFTFGPGTKVDIKRT", "cdrh1_seq": "GDSMSSYY", "cdrh2_seq": "ISTSGST", "cdrh3_seq": "ACSGSYSFFDY", "cdrl1_seq": "QDISNF", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYDNLRIFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 105]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "6phb", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2530", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "25 kDa ookinete surface antigen (Pfs25), Plasmodium falciparum", "target_domain": null, "functional_role": "other", "evidence_quote": "transmission-blocking antibody"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 21586, 1008, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 2637, 6713, 57, 7189, 2057, 3154, 4730, 12, 11133, 4198, 13, 1927, 15663, 13098, 18, 11133, 4198, 1977, 5822, 1990, 1920, 57, 7189, 2057, 3154, 2409, 1920, 8652, 11, 61, 2740, 1922, 1920, 9719, 21951, 18, 1920, 3533, 1977, 4609, 1966, 43, 5303, 17, 7472, 3533, 1988, 7042, 8652, 2740, 1922, 1920, 9719, 4580, 16, 2743, 1942, 43, 4008, 10095, 12, 3200, 23, 13, 1990, 1920, 11133, 4198, 4451, 1028, 3418, 18, 3], "antigen": ["ETGAKVTVDTVCKRGFLIQMSGHLECKCENDLVLVNEETCEEKVLKCDEKTVNKPCGDFSKCIKIDGNPVSYACKCNLGYDMVNNVCIPNECKQVTCGNGKCILDTSNPVKTGVCSCNIGKVPNVQDQNKCSKDGETKCSLKCLKEQETCKAVDGIYKCDCKDGFIIICT"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A cynomolgus macaque Fab, SKT-20 (IGHV4/IGKV2-Kappa), targeting the Coat protein of Venezuelan equine encephalitis virus. The Coat protein forms an icosahedral capsid with T=4 symmetry composed of 240 copies surrounded by a lipid membrane through which penetrate 80 spikes composed of trimers of E1-E2 heterodimers, and mediates viral attachment, entry, and immune evasion. The antibody is designed as a neutralizing antibody against Venezuelan equine encephalitis virus. What would the HCDRs be?", "target_protein": "QVQVQESGPGLVKPSETLSLTCAVSWTWIRQSPGKGLEWLGFFYNPSLESRVTISKDTSRNQFSLTLSSVSAADTAVYYCWGPGIRVTVSGSINDDSYYIHGGTGKSARSHFCSNTFCYGWFDV", "metadata": {"pdb_id": "8eev", "light_chain_seq": "VVMTQTPLSLPITPGEPASISCRSSQSLLHSNGNTYLHWYLQKPGQSPQLLIYGGSNRASGVPDRFSGSGSGTDFTLKISKVEAEDVGVYYCVQAIAFPWTFGQGTKVEI", "cdrh1_seq": "SGSINDDSYY", "cdrh2_seq": "IHGGTGKS", "cdrh3_seq": "ARSHFCSNTFCYGWFDV", "cdrl1_seq": "QSLLHSNGNTY", "cdrl2_seq": "GGS", "cdrl3_seq": "VQAIAFPWT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 59]", "cdrh3_pos": "[98, 114]", "cdrl1_pos": "[25, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "8eev", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "SKT-20", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Coat protein, Venezuelan equine encephalitis virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody against Venezuelan equine encephalitis virus"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 23836, 30351, 13057, 20533, 6914, 16, 3097, 1031, 17, 2036, 12, 20733, 1020, 1006, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 15642, 2213, 1927, 26803, 19240, 28965, 22279, 18744, 3413, 18, 1920, 15642, 2213, 4952, 1925, 29310, 24704, 14681, 1956, 62, 33, 24, 12572, 7179, 1927, 12075, 9425, 16006, 2007, 43, 4486, 3260, 2596, 2154, 21224, 3729, 14533, 7179, 1927, 28220, 1927, 11123, 17, 6602, 21523, 16, 1930, 10412, 4324, 8576, 16, 6904, 16, 1930, 3743, 25092, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 3316, 26803, 19240, 28965, 22279, 18744, 3413, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["YEHATTMPSQAGISYNTIVNRAGYAPLPISITPTKIKLIPTVNLEYVTCHYKTGMDSPAIKCCGSQECTPTYRPDEQCKVFTGVYPFMWGGAYCFCDTENTQVSKAYVMKSDDCLADHAEAYKAHTASVQAFLNITVGEHSIVTTVYVNGETPVNFNGVKITAGPLSTAWTPFDRKIVQYAGEIYNYDFPEYGAGQPGAFGDIQSRTVSSSDLYANTNLVLQRPKAGAIHVPYTQAPSGFEQWKKDKAPSLKFTAPFGCEIYTNPIRAENCAVGSIPLAFDIPDALFTRVSETPTLSAAECTLNECVYSSDFGGIATVKYSASKSGKCAVHVPSGTATLKEAAVELTEQGSATIHFSTANIHPEFRLQICTSYVTCKGDCHPPKDHIVTHPQYHAQTFTAA", "NEYKLTRPYMARCIRCAVGSCHSPIAIEAVKSDGHDGYVRLQTSSQYGLDGRTMRYDMHGTIKEIPLHQVSLYTSRPCHIVDGHGYFLLARCPAGDSITMEFKKDSVRHSCSVPYEVKFNPVGRELYTHPPEHGVEQACQVYAHDAQNRGAYVEMHLPDKWVYNSDKLPKAAGATLKGKLHVPFLLADGKCTVPLAPEPMITFGFRSVSLKLHPKNPTYLITRQLADEPHYTHELISEPAVRNFTVTEKGWEFVWGNHPPKRFWAQET"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A rat Fab (IGHV2/IGKV19-Kappa) targeting murine Neutrophil gelatinase-associated lipocalin (siderocalin), an iron-trafficking protein involved in innate immunity that binds iron through association with siderophores and modulates cellular iron levels. This antibody forms a complex with Neutrophil gelatinase-associated lipocalin. Please provide the HCDR sequences.", "target_protein": "ESLVQPSQTLSLTCTVSVHWVRQPPGQGLEWMGGDYNSALKSRLSISRDTSKSQVFLKMNSTDDTAIYFCWGQGASVTVSSAGFSLTSNSIWGDGRTTRCRRDSSYVVDA", "metadata": {"pdb_id": "3u9p", "light_chain_seq": "DILMTQSPLSLSASLGDKVTITCQASQIIYNYIAWYQQKPGKAPRLLIRYTSTLESGTPSRFSGSGSGRDYSFSISNVESEDIASYYCLQYDNLPYMFGAGTKLELKRA", "cdrh1_seq": "GFSLTSNS", "cdrh2_seq": "IWGDGRT", "cdrh3_seq": "TRCRRDSSYVVDA", "cdrl1_seq": "QIIYNY", "cdrl2_seq": "YTS", "cdrl3_seq": "LQYDNLPYM", "cdrh1_pos": "[17, 24]", "cdrh2_pos": "[42, 48]", "cdrh3_pos": "[85, 97]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3u9p", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGKV19", "is_engineered": false, "target_antigen": "Neutrophil gelatinase-associated lipocalin, Mus musculus", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 3067, 6914, 12, 20733, 15755, 19, 7021, 1040, 7390, 1026, 17, 12093, 13, 5133, 7135, 9460, 13200, 2051, 17, 2458, 3178, 5000, 1921, 12, 22940, 5000, 1921, 13, 16, 1925, 5680, 17, 9604, 2213, 3286, 1922, 8539, 7611, 1988, 6876, 5680, 2596, 3279, 1956, 22940, 14820, 1930, 13112, 3689, 5680, 2428, 18, 2052, 3533, 4952, 43, 2796, 1956, 9460, 13200, 2051, 17, 2458, 3178, 5000, 1921, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["LIPAPSLLTVPLQPDFRSDQFRGRWYVVGLAGNAVQKKGSFTMYSTIYELQENNSYNVTSILVCRYWIRTFVPSSRAGQFTLGNMHRYPQVQSYNVQVATTDYNQFAMVFFRKTSENKQYFKITLYGRTKELSPELKERFTRFAKSLGLKDDNIIFSVPTDQCIDN"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A human Fab, MJ20 (IGHV3/IGKV1-Kappa), targeting the C-terminal domain of Nucleoprotein from Reston ebolavirus. Nucleoprotein oligomerizes into a helical capsid to encapsidate the viral genome, protecting it from nucleases and the cellular innate immune response, and recruits host phosphatase to regulate viral transcription. The antibody is designed as a pan-specific diagnostic reagent capable of binding the C-terminal domains of nucleoproteins across all five known Ebola virus strains with high affinity. Please generate its HCDRs.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVASSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFNISYSSIYSYSGYTARSYWYHVGSWHYTGMDY", "metadata": {"pdb_id": "5w2b", "light_chain_seq": "QMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRT", "cdrh1_seq": "GFNISYSS", "cdrh2_seq": "IYSYSGYT", "cdrh3_seq": "ARSYWYHVGSWHYTGMDY", "cdrl1_seq": "QSVSSA", "cdrl2_seq": "SAS", "cdrl3_seq": "QQSSSSLIT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "5w2b", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "MJ20", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Nucleoprotein, Reston ebolavirus", "target_domain": null, "functional_role": "other", "evidence_quote": "pan-specific Fab with the ability to bind selectively to the C-terminal domains of the nucleoproteins from all five known strains of the Ebola virus"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 15697, 3520, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 45, 17, 4262, 3418, 1927, 2797, 6657, 2037, 6172, 1916, 24497, 11074, 18, 2797, 6657, 13034, 4517, 2460, 43, 11514, 14681, 1942, 10771, 21550, 1920, 4324, 3843, 16, 15145, 2176, 2037, 29305, 1930, 1920, 3689, 8539, 3743, 2644, 16, 1930, 18855, 4423, 8167, 1942, 5741, 4324, 3213, 18, 1920, 3533, 1977, 4609, 1966, 43, 3797, 17, 2487, 4785, 7916, 7131, 1927, 2743, 1920, 45, 17, 4262, 4682, 1927, 2797, 14070, 3436, 2136, 3628, 3171, 24497, 3413, 4046, 1956, 2149, 5173, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["KSMQKLEETYHHLLRTQGPFEAINYYHMMKDEPVIFSTDDGKEYTYPDSLEEAYPPWLTEKERLDKENRYIYINNQQFFWPVMSPRDKFLAILQHHQ"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A murine Fab, 4C1 (IGHV3/IGKV14-Kappa), targeting the Der p 1 allergen (Peptidase 1) of Dermatophagoides pteronyssinus. Der p 1 is a cysteine protease that cleaves and activates the host G protein-coupled receptor MRGPRX1 and elicits IgE responses in allergic subjects. The antibody is designed to recognize a cross-reactive IgE epitope on Der p 1, targeting surface-exposed residues that are molecular targets for allergen vaccine development.", "target_protein": "EVQLQESGPGLVKPSQSLSLTCTVTWNWIRQFPGNKLEWMGYSYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCWGQGTLVTVSAAGYSITSDYAISYSGTTGRTGVYRYPERAPY", "metadata": {"pdb_id": "5vph", "light_chain_seq": "QIVMTQSPFSMYATLGERVTITCKASQDIYSYLSWLQQKPGKSLKTLIYRANRLITGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPYTFGGGTKLEMKRA", "cdrh1_seq": "GYSITSDYA", "cdrh2_seq": "ISYSGTT", "cdrh3_seq": "GRTGVYRYPERAPY", "cdrl1_seq": "QDIYSY", "cdrl2_seq": "RAN", "cdrl3_seq": "LQYDEFPYT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5vpl", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "4C1", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV14", "is_engineered": false, "target_antigen": "Der p 1 allergen (Peptidase 1), Dermatophagoides pteronyssinus", "target_domain": null, "functional_role": "other", "evidence_quote": "binds to a unique cross-reactive epitope on both allergens associated with IgE recognition"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 8235, 1009, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 1006, 17, 12093, 13, 16, 5133, 1920, 3135, 58, 21, 15468, 12, 24050, 21, 13, 1927, 13467, 4965, 12363, 19147, 14186, 5590, 22214, 18, 3135, 58, 21, 1977, 43, 8666, 7154, 1988, 23839, 1930, 9094, 1920, 4423, 49, 2213, 17, 6416, 3148, 2852, 19874, 1005, 7653, 1930, 21809, 10777, 3387, 1922, 10519, 3297, 18, 1920, 3533, 1977, 4609, 1942, 9967, 43, 3567, 17, 6079, 10777, 10095, 1990, 3135, 58, 21, 16, 5133, 3154, 17, 4616, 4248, 1988, 2032, 3272, 4845, 1958, 15468, 5955, 2740, 18, 3], "antigen": ["TNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNANKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab, bH1 variant (IGHV3/IGKV1-Kappa), targeting the engineered Isoform L-VEGF206 of Vascular endothelial growth factor A. Vascular endothelial growth factor A is a growth factor active in angiogenesis and vasculogenesis that induces endothelial cell proliferation, promotes cell migration, inhibits apoptosis, and induces blood vessel permeabilization through binding to FLT1/VEGFR1, KDR/VEGFR2, and NRP1/neuropilin-1 receptors. This antibody forms a complex with the engineered VEGF antigen.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVARRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFNIKDTYIYPTNGYTAKLGIGYYYYGMDV", "metadata": {"pdb_id": "7kf1", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQDIPRSISGYVAWYQQKPGKAPKLLIYWGSYLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRT", "cdrh1_seq": "GFNIKDTY", "cdrh2_seq": "IYPTNGYT", "cdrh3_seq": "AKLGIGYYYYGMDV", "cdrl1_seq": "QDIPRSISGY", "cdrl2_seq": "WGS", "cdrl3_seq": "QQHYTTPPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "7kf1", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Isoform L-VEGF206 of Vascular endothelial growth factor A, Homo sapiens", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 9710, 1009, 6031, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 6174, 54, 17, 5785, 24238, 1927, 4541, 5003, 2905, 2991, 43, 18, 4541, 5003, 2905, 2991, 43, 1977, 43, 2905, 2991, 3500, 1922, 8244, 1930, 10205, 3761, 1988, 6387, 5003, 2024, 4031, 16, 7383, 2024, 5049, 16, 7042, 4091, 16, 1930, 6387, 2877, 8072, 22271, 2596, 2743, 1942, 29030, 1009, 19, 18828, 1009, 16, 29156, 19, 21609, 16, 1930, 5214, 5113, 19, 13889, 16207, 17, 21, 4086, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 11091, 5785, 4730, 18, 3], "antigen": ["EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A murine Fab (IGHV3/IGKV4-Kappa) targeting the Subtilisin-like protease 1 (SUB1) of Plasmodium falciparum. SUB1 is a serine protease that plays an essential role in merozoite invasion of and egress from host erythrocytes by processing and activating various merozoite surface and parasitophorous vacuole proteins. This antibody is intended as a structural tool to facilitate crystallization of the protease catalytic domain, binding within the Peptidase S8 domain.", "target_protein": "QVQLQESGPDLVKPSSSLKLTCTTTWHWIRQEPGKSLEWMGYDYNDSLKARITITRDTASNMFFLQLSSVTSDDTAVYYCWGAGTTVTVSSAGYSISSGYSIHYSGSTVIYRYDGQWVFDD", "metadata": {"pdb_id": "4lvn", "light_chain_seq": "DIVLTQSPATMSASLGQRVSMSCSASSSVSTSYFHWYQQKPGSSPKLWIYSTSNLASGVPGRFSGSGSGTSYSLSISSMEAEDAATYYCHQFHRSPLTFGAGTKLELKRA", "cdrh1_seq": "GYSISSGYS", "cdrh2_seq": "IHYSGST", "cdrh3_seq": "VIYRYDGQWVFDD", "cdrl1_seq": "SSVSTSY", "cdrl2_seq": "STS", "cdrl3_seq": "HQFHRSPLT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "4lvo", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Subtilisin-like protease 1, Plasmodium falciparum", "target_domain": "Peptidase S8", "functional_role": "structural_tool", "evidence_quote": "crystallization of recombinant PfSUB1 proved a substantial technical challenge, requiring production of a complex with a monoclonal antibody Fab fragment"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 7135, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1920, 14745, 1921, 17, 3189, 7154, 21, 12, 2316, 1009, 13, 1927, 15663, 13098, 18, 2316, 1009, 1977, 43, 8468, 7154, 1988, 5705, 1925, 4415, 2770, 1922, 6902, 26553, 6254, 1927, 1930, 15850, 1979, 2037, 4423, 14161, 2007, 4587, 1930, 8019, 3425, 6902, 26553, 3154, 1930, 16891, 22575, 2080, 20309, 2697, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 6628, 15416, 1927, 1920, 7154, 6804, 3418, 16, 2743, 2651, 1920, 24050, 13808, 3418, 18, 3], "antigen": ["HFNDEFRNLQWGLDLSRLDETQELINEHQVMSTRICVIDSGIDYNHPDLKDNIELNLKELHGRKGFDDDNNGIVDDIYGANFVNNSGNPMDDNYHGTHVSGIISAIGNNNIGVVGVDVNSKLIICKALDEHKLGRLGDMFKCLDYCISRNAHMINGSFSFDEYSGIFNSSVEYLQRKGILFFVSASNCSHPKSSTPDIRKCDLSINAKYPPILSTVYDNVISVANLKKNDNNNHYSLSINSFYSNKYCQLAAPGTNIYSTAPHNSYRKLNGTSMAAPHVAAIASLIFSINPDLSYKKVIQILKDSIVYLPSLKNMVAWAGYADINKAVNLAIKSKK"]} {"modality_type": "antibody", "text": "Output the HCDRs for an antibody that performs this function: A murine Fab (IGHV3/IGKV1-Kappa) targeting the engineered pH-gated potassium channel KcsA of Streptomyces lividans. The KcsA channel acts as a pH-gated potassium ion channel; changing cytosolic pH from 7 to 4 opens the channel, with monovalent cation preference K+ > Rb+ > NH4+ >> Na+ > Li+. This antibody is intended as a structural tool to stabilize and visualize the full-length channel in the open conformation, enabling mechanistic analysis of activation gating and allosteric coupling between the activation gate and selectivity filter.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVASYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFNISSYSISSYYSSTARQPSYHMYSWWVALDY", "metadata": {"pdb_id": "3pjs", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLESGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYYSYSAPVTFGQGTKVEIKRT", "cdrh1_seq": "GFNISSYS", "cdrh2_seq": "ISSYYSST", "cdrh3_seq": "ARQPSYHMYSWWVALDY", "cdrl1_seq": "QDVNTA", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYYSYSAPVT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "3pjs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "pH-gated potassium channel KcsA, Streptomyces lividans", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "Mechanism of Activation Gating in the Full-Length KcsA K+ Channel"}}}, "tokenized_instruction": [2, 6647, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 17436, 2052, 2347, 30, 43, 7135, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11091, 2087, 17, 12336, 9057, 4999, 29971, 1019, 1927, 22874, 15260, 9532, 3355, 18, 1920, 29971, 1019, 4999, 8016, 1966, 43, 2087, 17, 12336, 9057, 4755, 4999, 31, 8546, 9410, 2087, 2037, 27, 1942, 24, 19851, 1920, 4999, 16, 1956, 28685, 9976, 8308, 53, 15, 34, 6160, 15, 34, 14945, 15, 34, 34, 4049, 15, 34, 2336, 15, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 1930, 13159, 1920, 4125, 17, 3471, 4999, 1922, 1920, 4437, 7748, 16, 12180, 10640, 2333, 1927, 2936, 12568, 1930, 14772, 7590, 2192, 1920, 2936, 11898, 1930, 9008, 6199, 18, 3], "antigen": ["SALQWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRLVAVVVMVAGITSFGLVTAALATWFVGQEQQQQQQFVRHSEKAAEEAYTRTTRALHERFDRLERMLDDNRR"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A murine Fab, H5M9 (IGHV1/IGKV3-Kappa), targeting the Hemagglutinin of Influenza A virus (H5N1). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and is responsible for membrane fusion by releasing the fusion peptide in the endosome. The antibody is designed as a broadly neutralizing antibody against diverse H5N1 clades and subclades, targeting a conserved epitope in the HA1 vestigial esterase subdomain that is distinct from known antigenic sites and neutralizes by blocking both receptor binding and postattachment steps. Please provide the HCDR sequences.", "target_protein": "EVHLQQSGPELVKPGASVKMSCKTSIHWMKQSHGKSLEWIGGTYNQKFKVRATLTVGRSSSTAYMDLRSLTSEDSAVYYCWGAGTTVTVSSAGYTFTEYTIFPNNGDTVRNYGSSYGYFDV", "metadata": {"pdb_id": "4mhh", "light_chain_seq": "DIVLTQSPGSLTVSLGQRATISCRASESVDNFGKSFMHWYQQKPGQSPKLLIYRASNREFGIPARFNGSGSGTDFALTINPVEADDVATYFCQQSNEDPRTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTEYT", "cdrh2_seq": "IFPNNGDT", "cdrh3_seq": "VRNYGSSYGYFDV", "cdrl1_seq": "ESVDNFGKSF", "cdrl2_seq": "RAS", "cdrl3_seq": "QQSNEDPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "8g5b", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "H5M9", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing murine monoclonal antibody, H5M9, to most H5N1 clades and subclades"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 7135, 6914, 16, 14106, 1035, 1026, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 12, 20128, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 1977, 5061, 1958, 3260, 5289, 2007, 13182, 1920, 5289, 4207, 1922, 1920, 22321, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 3316, 6445, 20128, 15961, 1930, 8959, 6363, 16, 5133, 43, 5305, 10095, 1922, 1920, 2118, 1009, 5634, 2677, 2086, 26389, 27517, 1988, 1977, 4493, 2037, 3171, 14606, 3402, 1930, 25885, 1036, 2007, 7472, 2321, 3148, 2743, 1930, 2753, 29416, 2072, 2017, 5983, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["DPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab, H014 (IGHV1/IGKV6-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors (primarily ACE2) to initiate infection, and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that prevents SARS-CoV-2 attachment to host cell receptors by engaging the receptor-binding domain in its open conformation.", "target_protein": "VQLVQSGAEVKKPGATVKISCKVSIHWVKQAPGKSLEWIGYSDNLKFKGAATLTADTSTDTAYMELSSLRSEDTAVYYCWGQGTTVTVSSAGYSFSNYYIDPFNGGTARSEYDPYYVMDY", "metadata": {"pdb_id": "7cak", "light_chain_seq": "IVLTQSPFQSVSPKEKVTITCRASQSISSNLHWYQQKPDQSPKLLIKYASQSISGIPSRFSGSGSGTDFTLTINSLEAEDFGIYFCQQTNFWPYIFGQGTKLEILKR", "cdrh1_seq": "GYSFSNYY", "cdrh2_seq": "IDPFNGGT", "cdrh3_seq": "ARSEYDPYYVMDY", "cdrl1_seq": "QSISSN", "cdrl2_seq": "YAS", "cdrl3_seq": "QQTNFWPYI", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 107]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "7cak", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "H014", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "efficiently neutralizes SARS-CoV-2 and prevents attachment to host cell receptors"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 29161, 3745, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 12, 5985, 8298, 1028, 13, 1942, 11051, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 10299, 20466, 17, 6083, 17, 22, 8576, 1942, 4423, 2024, 4086, 2007, 15888, 1920, 3148, 17, 2743, 3418, 1922, 2496, 4437, 7748, 18, 3], "antigen": ["PPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A human Fab, EEEV-143 (IGHV3/IGKV3-Kappa), targeting the Togavirin structural polyprotein of Eastern equine encephalitis virus. The Togavirin forms an icosahedral capsid with 80 spikes composed of trimers of E1-E2 heterodimers that mediate viral attachment and entry into host cells. The antibody is designed as a neutralizing antibody targeting domain B of the E2 glycoprotein, with the objective of preventing viral entry through engagement of the trimeric E2 spike architecture.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASIHWVRQAPGKGLEWVAVYIADPVKGRFTISRDNSKNMLYLQMNSLRTEDTAVYYCWGQGIPVTVSSAGFTFSNYGISYDGRHKAKDTSGWYEFFDS", "metadata": {"pdb_id": "6xob", "light_chain_seq": "EIVMTQSPATLSVSPGERATLSCRASQSVATNVAWYQQKPGQAPRLLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQCNDWLTFGQGTKVEIKRT", "cdrh1_seq": "GFTFSNYG", "cdrh2_seq": "ISYDGRHK", "cdrh3_seq": "AKDTSGWYEFFDS", "cdrl1_seq": "QSVATN", "cdrl2_seq": "GAS", "cdrl3_seq": "QQCNDWLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6xob", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "EEEV-143", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Togavirin (Structural polyprotein), Eastern equine encephalitis virus", "target_domain": "Domain B of E2 glycoprotein", "functional_role": "neutralizing", "evidence_quote": "potently neutralizing human anti-EEEV mAb...mediated 100% survival...against WT EEEV aerosol challenge"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 2616, 6914, 16, 11150, 9488, 17, 13370, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 4068, 23409, 4346, 6240, 5684, 1927, 11562, 22279, 18744, 3413, 18, 1920, 4068, 23409, 4952, 1925, 29310, 24704, 14681, 1956, 3729, 14533, 7179, 1927, 28220, 1927, 11123, 17, 6602, 21523, 1988, 8265, 4324, 8576, 1930, 6904, 2460, 4423, 2094, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 3418, 44, 1927, 1920, 6602, 11424, 16, 1956, 1920, 4470, 1927, 8444, 4324, 6904, 2596, 9577, 1927, 1920, 29177, 6602, 10429, 9335, 18, 3], "antigen": ["DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGVDLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRHTCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSIHSAKVKITVPSGAQVKYYCKCPDVRKGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRLPRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSDANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRYPLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCC"]} {"modality_type": "antibody", "text": "Output the HCDRs for an antibody that performs this function: A human Fab, C1533 (IGHV1/IGLV1-Lambda), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding or proteolytic cleavage. The antibody is designed as a neutralizing antibody targeting the N-terminal domain (NTD), with breadth against SARS-CoV-2 variants of concern.", "target_protein": "VQLVQSGAEVKKPGSSVKVSCKTSFSWVRQAPGQGLEWMGRNSAQEFQGRVTLNADKSTSTVYMELSSLRSEDTAIYYCWGQGTTVTVSSGVIFSRNAIIPFLDVTARHNGDPYDFWSGYNTWAGGLDV", "metadata": {"pdb_id": "9bj2", "light_chain_seq": "LTQPPSASGTPGQRVTISCSGSGSNIGSNAVNWYQQLPGTAPKLLIYNQNQRPSGVPDRFSGSKSGTSASLAIGGLQSEDEADYYCATWDDNLSGLVFGGGTKLTVLG", "cdrh1_seq": "GVIFSRNA", "cdrh2_seq": "IIPFLDVT", "cdrh3_seq": "ARHNGDPYDFWSGYNTWAGGLDV", "cdrl1_seq": "GSNIGSNA", "cdrl2_seq": "NQN", "cdrl3_seq": "ATWDDNLSGLV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 117]", "cdrl1_pos": "[22, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7l2f", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "C1533", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "N-terminal domain (NTD)", "functional_role": "neutralizing", "evidence_quote": "NTD-specific antibody displayed breadth of binding to VOCs; NTD-RBD bsAbs retained potent neutralization activity against Omicron variants"}}}, "tokenized_instruction": [2, 6647, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 17436, 2052, 2347, 30, 43, 2616, 6914, 16, 29832, 6498, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 2014, 12712, 6404, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 56, 17, 4262, 3418, 12, 22078, 13, 16, 1956, 22532, 3316, 20466, 17, 6083, 17, 22, 4936, 1927, 8353, 18, 3], "antigen": ["QCVNLTAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLKNLREFVFKNIDGYFKIYSKHTPINDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTL"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A Fab (IGHV4/IGLV9-Lambda) targeting the VP8* fragment of the Outer capsid protein VP4 of Rotavirus A. The antibody is designed as a neutralizing antibody capable of neutralizing human rotavirus in intestinal epithelial cells and conferring protection against rotavirus-induced diarrhea, binding within the Haemagglutinin outer capsid protein VP4 concanavalin-like domain.", "target_protein": "QVQLQESGPGLVKPSQTLSLTCSVSWNWIRQPAGKGLEWIGRNYNPSLKGRLTMSIDTSKNQLSLRLSSVTAADTAVYYCWGQGTPVTVSSGVSLSGGSYTIFTSGSTVADYYYSVPDV", "metadata": {"pdb_id": "6pcu", "light_chain_seq": "QPVLTQPPSASASLGASVTLTCTLSSGYSNYKVDWYQQRPGKGPRFVMRVGTGGIVGSKGDGIADRFSVSGSGLNRSLTIKNIQEEDESDYHCGADHGSGDNFVRVFGGGTKLTVL", "cdrh1_seq": "GVSLSGGSYT", "cdrh2_seq": "IFTSGST", "cdrh3_seq": "VADYYYSVPDV", "cdrl1_seq": "SGYSNYK", "cdrl2_seq": "VGTGGIVG", "cdrl3_seq": "GADHGSGDNFVRV", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 107]", "cdrl1_pos": "[25, 31]", "cdrl2_pos": "[49, 56]", "cdrl3_pos": "[93, 105]", "cdrh3_split": "val", "cdrh3_cluster": "6pcu", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGLV9", "is_engineered": false, "target_antigen": "Outer capsid protein VP4, Rotavirus A", "target_domain": "Haemagglutinin outer capsid protein VP4 concanavalin-like", "functional_role": "neutralizing", "evidence_quote": "VP8* mAbs efficiently neutralized human RV in HT-29 cells or enteroids and protected suckling mice from diarrhea"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 6914, 12, 20733, 1020, 1006, 19, 28961, 1020, 1026, 17, 18279, 13, 5133, 1920, 9314, 1025, 14, 5302, 1927, 1920, 7642, 14681, 2213, 9314, 1006, 1927, 20456, 43, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 7131, 1927, 12130, 2616, 20456, 1922, 6139, 4944, 2094, 1930, 21510, 6202, 3316, 20456, 17, 2719, 11904, 16, 2743, 2651, 1920, 7105, 17003, 1921, 7642, 14681, 2213, 9314, 1006, 2499, 7241, 4701, 1921, 17, 3189, 3418, 18, 3], "antigen": ["SILDGPYQPTTFKPPNDYWLLISSNTDGVVYESTNNSDFWTAVIAVEPHVSQTNRQYVLFGENKQFNVENSSDKWKFFEMFKGSSQSDFSNRRTLTSNNRLVGMLKYGGRVWTFHGETPRATTDSSNTADLNNISIIIHSEFYIIPRSQESKCNEYINNGL"]} {"modality_type": "antibody", "text": "I want an antibody that has the function: A murine Fab, 2C11 (IGHV1/IGKV12-Kappa), targeting an engineered isoform 2 of Protein-serine O-palmitoleoyltransferase porcupine from Homo sapiens. Porcupine is a key regulator of the Wnt signaling pathway that mediates the attachment of palmitoleate to Wnt proteins, a modification required for efficient binding to frizzled receptors. The antibody is designed as a structural tool to stabilize native PORCN for cryo-electron microscopy studies of substrate-bound and inhibitor-bound states. Output the HCDRs.", "target_protein": "EIQLQQSGAELVKPGASVKMSCKVSMNWVKQSHGKSLEWIGNNYNQKFTGKATFTVDRSSSTAYMQLDSLTSEDSAVYYCWGQGTLVTVSSGYSFTGYNINPYYVSTARSYGSSHTFAY", "metadata": {"pdb_id": "7urc", "light_chain_seq": "DIHMTQSPASLSAFVGETVTITCRTSENIFSYLAWYQQKQGKSPQLLVYNAKTLTSGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGSPYTFGGGTKLEIK", "cdrh1_seq": "GYSFTGYN", "cdrh2_seq": "INPYYVST", "cdrh3_seq": "ARSYGSSHTFAY", "cdrl1_seq": "ENIFSY", "cdrl2_seq": "NAK", "cdrl3_seq": "QHHYGSPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7ura", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2C11", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV12", "is_engineered": true, "target_antigen": "Protein-serine O-palmitoleoyltransferase porcupine (isoform 2), Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "monoclonal antibody denoted 2C11 that explicitly binds to native PORCN...to capture the substrate-bound state"}}}, "tokenized_instruction": [2, 51, 12914, 1925, 3533, 1988, 2258, 1920, 2347, 30, 43, 7135, 6914, 16, 6921, 3242, 12, 20733, 7390, 19, 7021, 1040, 7390, 1028, 17, 12093, 13, 16, 5133, 1925, 11091, 6174, 22, 1927, 2213, 17, 8468, 57, 17, 13615, 2456, 10921, 9961, 4572, 18021, 12184, 2037, 16350, 27974, 18, 4572, 18021, 12184, 1977, 43, 3834, 7888, 1927, 1920, 7028, 3197, 3374, 1988, 10412, 1920, 8576, 1927, 13615, 2456, 2010, 1942, 7028, 2697, 16, 43, 6295, 3414, 1958, 5807, 2743, 1942, 9081, 18559, 2824, 4086, 18, 1920, 3533, 1977, 4609, 1966, 43, 4346, 5229, 1942, 13448, 6196, 4572, 7814, 1958, 15822, 17, 4995, 5441, 2351, 1927, 4510, 17, 4124, 1930, 4106, 17, 4124, 4376, 18, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["FSRQEFFQQLLQGCLLPTAQQGLDQIWLLLAICLACRLLWRLGLPSYLKHASTVAGGFFSLYHFFQLHMVWVVLLSLLCYLVLFLCRHSSHRGVFLSVTILIYLLMGEMHMVDTVTWHKMRGAQMIVAMKAVSLGFDLDRGEVGTVPSPVEFMGYLYFVGTIVFGPWISFHSYLQAVQGRPLSCRWLQKVARSLALALLCLVLSTCVGPYLFPYFIPLNARWLRAYESAVSFHFSNYFVGFLSEATATLAGAGFTEEKDHLEWDLTVSKPLNVELPRSMVEVVTSWNLPMSYWLNNYVFKNALRLGTFSAVLVTYAASALLHGFSFHLAAVLLSLAFITYVEHVLRKRLARILSACVLSKRCPPDCSHQHRLGLGVRALNLLFGALAIFHLAYLGSLFDVYGMAYTVHKWSELSWASHWVTFGCWIFYRLIG"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, ARGX-121 (IGHV3/IGLV1-Lambda), targeting the Fc fragment of IgA1, specifically the Immunoglobulin heavy constant alpha 1 domain. The constant region of immunoglobulin heavy chains mediates the effector phase of humoral immunity through interaction with Fc receptors and other immune components. This antibody forms a complex with the Fc fragment of IgA1.", "target_protein": "EVQLLESGGGLVQPGGSLRLSCAASMSWVRQAPGKGLEWVSSYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTSSNYLIYHYGHNAAKVDSAYDFGS", "metadata": {"pdb_id": "9r2e", "light_chain_seq": "SVLTQPPSVSGAPGQRVTISCAGTSSDIGGRTYVSWYQQLPGTAPKLLIYKVTIRASGVPDRFSGSKSGTSASLAITGLQAEDEADYYCASHRSNNNIVFGGGTKLTVLGQ", "cdrh1_seq": "GFTSSNYL", "cdrh2_seq": "IYHYGHNA", "cdrh3_seq": "AKVDSAYDFGS", "cdrl1_seq": "SSDIGGRTY", "cdrl2_seq": "KVT", "cdrl3_seq": "ASHRSNNNIV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "9r2e", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ARGX-121", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "Immunoglobulin heavy constant alpha 1, Homo sapiens", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 4582, 1039, 17, 11844, 12, 20733, 1020, 1010, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 6437, 5302, 1927, 12114, 1009, 16, 4475, 1920, 11837, 7881, 5168, 4595, 21, 3418, 18, 1920, 5168, 3031, 1927, 11837, 7881, 7835, 10412, 1920, 7917, 3193, 1927, 16601, 7611, 2596, 2835, 1956, 6437, 4086, 1930, 2303, 3743, 4178, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 6437, 5302, 1927, 12114, 1009, 18, 3], "antigen": ["CHPRLSLHRPALEDLLLGSEANLTCTLTGVTFTWTPSSGKSAVQGPPECGCYSVSSVLPGCAEPWNHGKTFTCTAAYPESKTPLTATLSKSGNTFRPEVHLLPPPSEELALNELVTLTCLARGFSPKDVLVRWLQGSQELPREKYLTWASRQEPSQGTTTFAVTSILRVAAEDWKKGDTFSCMVGHEALPLAFTQKTIDRLA"]} {"modality_type": "antibody", "text": "Here is the antibody function: A murine Fab, ICSM 18 (IGHV1/IGKV4-Kappa), targeting the Major prion protein of Homo sapiens. The Major prion protein plays roles in neuronal development, synaptic plasticity, myelin maintenance, and iron homeostasis. The antibody is designed to bind the native PrP C conformation with high affinity to prevent conversion to disease-related PrP Sc conformers and cure prion-infected cells, binding within the Interaction with GRB2, ERI3 and SYN1. Generate the corresponding HCDRs.", "target_protein": "EVQLQQSGPELVKPGSSVKISCKASLDWVKQSHGKTLEWIGNGYNQKFRGKATLTVDKSSSTAYMELHSLTSEDSAVYYCWGQGTLVTVSSARNTFTDYNVYPNNGVTALYYYDVSY", "metadata": {"pdb_id": "2w9e", "light_chain_seq": "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMHWYQQKSGTSPKRWIYDTSKLASGVPARFSGSGSGTSYSLTISSMEAEDAATYFCHQWRSNPYTFGGGTKLEIKRA", "cdrh1_seq": "RNTFTDYN", "cdrh2_seq": "VYPNNGVT", "cdrh3_seq": "ALYYYDVSY", "cdrl1_seq": "SSVSY", "cdrl2_seq": "DTS", "cdrl3_seq": "HQWRSNPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 104]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "2w9e", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ICSM 18", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Major prion protein, Homo sapiens", "target_domain": "Interaction with GRB2, ERI3 and SYN1", "functional_role": "other", "evidence_quote": "ability of an antibody to cure prion-infected cells correlates with its binding affinity for PrP C"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 7135, 6914, 16, 13772, 1035, 2654, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 16, 5133, 1920, 3044, 16686, 2213, 1927, 16350, 27974, 18, 1920, 3044, 16686, 2213, 5705, 5456, 1922, 5121, 2740, 16, 6251, 8771, 16, 12996, 6291, 16, 1930, 5680, 7622, 18, 1920, 3533, 1977, 4609, 1942, 4566, 1920, 6196, 11533, 45, 7748, 1956, 2149, 5173, 1942, 4625, 7309, 1942, 2573, 17, 2712, 11533, 2160, 27757, 1930, 12338, 16686, 17, 4014, 2094, 16, 2743, 2651, 1920, 2835, 1956, 28544, 16, 2668, 1033, 1010, 1930, 2540, 1009, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["LGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQ"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A human Fab, 2F5 (IGHV2/IGKV1-Kappa), targeting the membrane-proximal external region (MPER) of gp41 from Human immunodeficiency virus 1. The gp41 MPER is a conserved region that mediates fusion between viral and host cell membranes during entry. The antibody is designed as a broadly neutralizing antibody that prevents membrane fusion by targeting the MPER epitope, binding within the Membrane-proximal external region (MPER).", "target_protein": "RITLKESGPPLVKPTQTLTLTCSFSVGWIRQPPGKALEWLAIRYSPSLNTRLTITKDTSKNQVVLVMTRVSPVDTATYFCWGQGITVTISSTGFSLSDFGVGIYSDDDKAHRRGPTARGPVNAMDV", "metadata": {"pdb_id": "3d0l", "light_chain_seq": "ALQLTQSPSSLSASVGDRITITCRASQGVTSALAWYRQKPGSPPQLLIYDASSLESGVPSRFSGSGSGTEFTLTISTLRPEDFATYYCQQLHFYPHTFGGGTRVDVRRT", "cdrh1_seq": "GFSLSDFGVG", "cdrh2_seq": "IYSDDDK", "cdrh3_seq": "AHRRGPTARGPVNAMDV", "cdrl1_seq": "QGVTSA", "cdrl2_seq": "DAS", "cdrl3_seq": "QQLHFYPHT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 113]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3d0l", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2F5", "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "gp41 fusion peptide-membrane-proximal external region (FP-MPER), Human immunodeficiency virus 1", "target_domain": "Membrane-proximal external region (MPER)", "functional_role": "neutralizing", "evidence_quote": "potent and broadly neutralizing activity against HIV-1, interferes with fusion between viral and host cell membranes"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 13775, 1015, 12, 20733, 15755, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 1927, 25618, 2037, 2616, 13141, 3413, 21, 18, 1920, 25618, 5438, 1915, 1977, 43, 5305, 3031, 1988, 10412, 5289, 2192, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1988, 10299, 3260, 5289, 2007, 5133, 1920, 5438, 1915, 10095, 16, 2743, 2651, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 18, 3], "antigen": ["LELDKWASLW"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human Fab, 14G6 (IGHV1/IGKV6-Kappa), targeting Bcl-2 homologous antagonist/killer (BAK), a human pro-apoptotic protein that promotes mitochondrial outer membrane permeabilization by oligomerizing to form pores and releasing apoptogenic factors. The antibody is designed to selectively recognize and stabilize the non-activated BAK conformer, inhibiting the unfolding and conformational changes required for BAK activation and pore formation. Please generate the HCDRs for this antibody.", "target_protein": "EVKLVESGAELVRPGTSVKVSCKASIEWVKQRPGQGLEWIGVNYNEKFKGKATLTADKSSSTAYMQLTSLTSDDSAVYFCWGQGTTVTVSSAGYAFTNYLINPGSGGTASPSLYGSFDY", "metadata": {"pdb_id": "8uky", "light_chain_seq": "DIVMTQSHKFMSTSVGDRVSITCKASQDVGTAVAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYSSYRTFGGGTKLEIKRT", "cdrh1_seq": "GYAFTNYL", "cdrh2_seq": "INPGSGGT", "cdrh3_seq": "ASPSLYGSFDY", "cdrl1_seq": "QDVGTA", "cdrl2_seq": "WAS", "cdrl3_seq": "QQYSSYRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "8uky", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "14G6", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": false, "target_antigen": "Bcl-2 homologous antagonist/killer, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "inhibited BAK unfolding triggered by BAK activators, preventing activation"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 2607, 1029, 1016, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 6717, 17, 22, 8725, 8151, 19, 16644, 12, 15600, 13, 16, 43, 2616, 1965, 17, 6353, 2213, 1988, 7383, 4596, 7642, 3260, 22271, 2007, 13034, 3903, 1942, 2386, 14711, 1930, 13182, 3588, 3880, 2790, 18, 1920, 3533, 1977, 4609, 1942, 9331, 9967, 1930, 13448, 1920, 2447, 17, 4128, 15600, 4955, 1915, 16, 7918, 1920, 17490, 1930, 8523, 2840, 3414, 1958, 15600, 2936, 1930, 8554, 3337, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["SMSEEQVAQDTEEVFRSYVFYRHQQEQEAEGPSSTMGQVGRQLAIIGDDINRRYDSEFQTMLQHLQPTAENAYEYFTKIATSLFESGINWGRVVALLGFGYRLALHVYQHGLTGFLGQVTRFVVDFMLHHSIARWIAQRGGWVAALNL"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A synthetic Fab (IGHV3/IGKV1-Kappa) targeting the pH-gated potassium channel KcsA of Streptomyces lividans. The KcsA channel acts as a pH-gated potassium ion channel that opens when cytosolic pH changes from 7 to 4, with monovalent cation preference K+ > Rb+ > NH4+ >> Na+ > Li+. This engineered Fab is designed as a structural biology tool for crystallization and cryo-EM studies, binding to the conserved turret loop of KcsA to stabilize the channel and facilitate crystal formation.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWIGENYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGYTFTSDWIIPSYGRAARERGDGYFDY", "metadata": {"pdb_id": "7mdj", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSIGTDIHWYQQKPGKAPKLLIKYASESISGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSNRWPFTFGQGTKVEIKRT", "cdrh1_seq": "GYTFTSDW", "cdrh2_seq": "IIPSYGRA", "cdrh3_seq": "ARERGDGYFDY", "cdrl1_seq": "QSIGTD", "cdrl2_seq": "YAS", "cdrl3_seq": "QQSNRWPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7mdj", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "pH-gated potassium channel KcsA, Streptomyces lividans", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "engineered synthetic Fab used as a crystallization chaperone to obtain crystals of the KcsA channel"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 6830, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 2087, 17, 12336, 9057, 4999, 29971, 1019, 1927, 22874, 15260, 9532, 3355, 18, 1920, 29971, 1019, 4999, 8016, 1966, 43, 2087, 17, 12336, 9057, 4755, 4999, 1988, 19851, 2469, 9410, 2087, 2840, 2037, 27, 1942, 24, 16, 1956, 28685, 9976, 8308, 53, 15, 34, 6160, 15, 34, 14945, 15, 34, 34, 4049, 15, 34, 2336, 15, 18, 2052, 11091, 6914, 1977, 4609, 1966, 43, 4346, 7256, 5229, 1958, 15416, 1930, 15822, 17, 2391, 2351, 16, 2743, 1942, 1920, 5305, 7431, 10411, 5881, 1927, 29971, 1019, 1942, 13448, 1920, 4999, 1930, 6628, 6561, 3337, 18, 3], "antigen": ["SALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALATWFVGREQERRG"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A murine Fab, ACT-1 (IGHV1/IGKV1-Kappa), targeting the integrin alpha-4/beta-7 (\u03b14\u03b27) heterodimer of Homo sapiens. The integrin \u03b14\u03b27 mediates lymphocyte migration and homing to gut-associated lymphoid tissue through interactions with mucosal adhesion molecules including MAdCAM-1, VCAM1, and fibronectin. The antibody is designed to modulate integrin function by binding the \u03b14\u03b27 headpiece in a manner that preserves the intermediate conformational state supporting rolling adhesion. Please output the HCDRs.", "target_protein": "QVQLQQPGAELVKPGTSVKLSCKGYMHWVKQRPGQGLEWIGENYNQKFKGKATLTVDISSSTAYMQLSSLTSEDSAVYYCWGQGTSVTVSSAGYTFTSYWIDPSESNTARGGYDGWDYAIDY", "metadata": {"pdb_id": "3v4p", "light_chain_seq": "DVVVTQTPLSLPVSFGDQVSISCRSSQSLAKSYGNTYLSWYLHKPGQSPQLLIYGISNRFSGVPDRFSGSGSGTDFTLKISTIKPEDLGMYYCLQGTHQPYTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTSYW", "cdrh2_seq": "IDPSESNT", "cdrh3_seq": "ARGGYDGWDYAIDY", "cdrl1_seq": "QSLAKSYGNTY", "cdrl2_seq": "GIS", "cdrl3_seq": "LQGTHQPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "3v4p", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Integrin alpha-4/beta-7 (\u03b14\u03b27), Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "therapeutic Fabs bind \u03b1(4)\u03b2(7) lymphocyte homing receptor"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 4033, 17, 21, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 8920, 4595, 17, 24, 19, 4666, 17, 27, 12, 17623, 1110, 1027, 13, 15672, 1927, 16350, 27974, 18, 1920, 8920, 17623, 1110, 1027, 10412, 10009, 5049, 1930, 20621, 1942, 7660, 17, 2458, 11751, 2960, 2596, 3719, 1956, 9565, 6141, 4206, 2710, 9133, 15024, 17, 21, 16, 19942, 1009, 16, 1930, 12848, 18, 1920, 3533, 1977, 4609, 1942, 8480, 8920, 2347, 2007, 2743, 1920, 17623, 1110, 1027, 4469, 10984, 12761, 1922, 43, 5222, 1988, 29256, 1920, 6129, 8523, 3360, 6184, 21691, 6141, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["RGQQEVLQDQPLSQGARGEGATQLAPQRVRVTLRPGEPQQLQVRFLRAEGYPVDLYYLMDLSYSMKDDLERVRQLGHALLVRLQEVTHSVRIGFGSFVDKTVLPFVSTVPSKLRHPCPTRLERCQSPFSFHHVLSLTGDAQAFEREVGRQSVSGNLDSPEGGFDAILQAALCQEQIGWRNVSRLLVFTSDDTFHTAGDGKLGGIFMPSDGHCHLDSNGLYSRSTEFDYPSVGQVAQALSAANIQPIFAVTSAALPVYQELSKLIPKSAVGELSEDSSNVVQLIMDAYNSLSSTVTLEHSSLPPGVHISYESQCEGPEKREGKAEDRGQCNHVRINQTVTFWVSLQATHCLPEPHLLRLRALGFSEELIVELHTLC", "YNVDTESALLYQGPHNTLFGYSVVLHSHGANRWLLVGAPTANWLANASVINPGAIYRCRIGKNPGQTCEQLQLGSPNGEPCGKTCLEERDNQWLGVTLSRQPGENGSIVTCGHRWKNIFYIKNENKLPTGGCYGVPPDLRTELSKRIAPCYQDYVKKFGENFASCQAGISSFYTKDLIVMGAPGSSYWTGSLFVYNITTNKYKAFLDKQNQVKFGSYLGYSVGAGHFRSQHTTEVVGGAPQHEQIGKAYIFSIDEKELNILHEMKGKKLGSYFGASVCAVDLNADGFSDLLVGAPMQSTIREEGRVFVYINSGSGAVMNAMETNLVGSDKYAARFGESIVNLGDIDNDGFEDVAIGAPQEDDLQGAIYIYNGRADGISSTFSQRIEGLQISKSLSMFGQSISGQIDADNNGYVDVAVGAFRSDSAVLLRTRPVVIVDASLSHPESVNRTKFDCVENGWPSVCIDLTLCFSYKGKEVPGYIVLFYNMSLDVNRKAESPPRFYFSSNGTSDVITGSIQVSSREANCRTHQAFMRKDVRDILTPIQIEAAYHLGPHSTEEFPPLQPILQQKKEKDIMKKTINFAR"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A murine Fab (IGHV5/IGKV4-Kappa) targeting an engineered fragment of Apical membrane antigen 1 (AMA1) from Plasmodium vivax Sal-1. AMA1 plays a vital role in the invasion of the host erythrocyte by the malaria parasite, interacting with RON2 during the invasion process. The antibody is designed to block invasion by stabilizing the D2 loop conformation and preventing its displacement, thereby precluding RON2 receptor engagement. Please provide the HCDR sequences.", "target_protein": "EVQLVESGGGLVKPGGSLKLSCAASMYWVRQTPEKRLEWVATYYPDSVKGRFTISRDNAKNNLYLQMSSLKSEDTAMYFCWGQGTLVTVSAAGFTFSDYYINDGGTYTARGSQLGRGEFAY", "metadata": {"pdb_id": "8rek", "light_chain_seq": "IVLSQSPAILSASPGEKVTMTCRASSSVSYMHWYQQKPGSSPKPWIYATFNLASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQWSSNPPTFGAGTKLELKRA", "cdrh1_seq": "GFTFSDYY", "cdrh2_seq": "INDGGTYT", "cdrh3_seq": "ARGSQLGRGEFAY", "cdrl1_seq": "SSVSY", "cdrl2_seq": "ATF", "cdrl3_seq": "QQWSSNPPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[25, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "8rek", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV4", "is_engineered": true, "target_antigen": "Apical membrane antigen 1 (Fragment), Plasmodium vivax Sal-1", "target_domain": null, "functional_role": "other", "evidence_quote": "antibody prevents displacement of the D2 loop as well as blocking the exposed region of the RON2-binding site, thus completely precluding engagement with the receptor"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 7135, 6914, 12, 20733, 1020, 1015, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1925, 11091, 5302, 1927, 8913, 3260, 4730, 21, 12, 2150, 4904, 13, 2037, 15663, 20236, 3370, 17, 21, 18, 2150, 4904, 5705, 43, 8970, 2770, 1922, 1920, 6254, 1927, 1920, 4423, 15469, 2007, 1920, 7505, 8652, 16, 8615, 1956, 25851, 1028, 2409, 1920, 6254, 2585, 18, 1920, 3533, 1977, 4609, 1942, 3367, 6254, 2007, 14384, 1920, 8631, 5881, 7748, 1930, 8444, 2496, 9514, 16, 6113, 8395, 9062, 25851, 1028, 3148, 9577, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["TVERSTRMGNPWKAFMEKYDIERTHSSGVRVDLGEDAEVENAKYRIPAGRCPVFGKGIVIENSDVSFLRPVATGDQKLKDGGFAFPNANDHISPMTLANLKERYKDNVEMMKLNDIALCRTHAASFVSNYRHPAVYDEKEKTCHMLYLSAQENMGPRYCSPDAVFCFKPDKDESFENLVYLSKNVRNDWDKKCPRKNLGNAKFGLWVDGNCEEIPYVKEVEAEDLRECNRIVFGASASDQKIQQGFRQNNREMIKSAFLPVDNFKSKGRGFNWANFDSVKKKCYIFNTKPTCLINDKNFIATTALSHPQEVDLEFPCSIYKDEIEREIKKQSSVDGERIVLPRIFISNDKESIKCPCEPERISQSTCNFYVCNCVEKRAEIKENNQVVIKEEFRNYY"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab, CIS42 (IGHV7/IGLV2-Lambda), targeting the Circumsporozoite protein of Plasmodium falciparum. The Circumsporozoite protein is an essential sporozoite protein required for sporozoite migration through the host dermis and infection of host hepatocytes, and binds to highly sulfated heparan sulfate proteoglycans on the surface of host hepatocytes. This antibody forms a complex with PfCSP peptide 21, a peptide derived from the central repeat region of the Circumsporozoite protein.", "target_protein": "VQLVQSGSELKKPGASVKVSCKTSMNWVRQAPGQGLEWMGWTYAPGFTGRFVFSFDTSVSTAYLQISSLKAEDTAVYYCWGQGTLVTVSSAGYTFTTYAINTNTGNPARVYSYGVPFDY", "metadata": {"pdb_id": "6b5r", "light_chain_seq": "QSVLTQPASVSGSPGQSITISCTATSSNVGSFNLVSWYQHHPGKAPKLIIHEVSKRPSGASNRFSGSKSGNTASLTISGLQAEDEADYYCCSYVGSDTWVFGGGTKLTVLGQ", "cdrh1_seq": "GYTFTTYA", "cdrh2_seq": "INTNTGNP", "cdrh3_seq": "ARVYSYGVPFDY", "cdrl1_seq": "SSNVGSFNL", "cdrl2_seq": "EVS", "cdrl3_seq": "CSYVGSDTWV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 106]", "cdrl1_pos": "[25, 33]", "cdrl2_pos": "[51, 53]", "cdrl3_pos": "[90, 99]", "cdrh3_split": "val", "cdrh3_cluster": "6b5r", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CIS42", "antibody_format": "Fab", "heavy_subclass": "IGHV7", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Circumsporozoite protein, Plasmodium falciparum", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 16, 5848, 6852, 12, 20733, 1020, 1027, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 28868, 2074, 26553, 2213, 1927, 15663, 13098, 18, 1920, 28868, 2074, 26553, 2213, 1977, 1925, 4415, 9130, 26553, 2213, 3414, 1958, 9130, 26553, 5049, 2596, 1920, 4423, 20201, 1930, 2909, 1927, 4423, 9919, 16, 1930, 6876, 1942, 3626, 26649, 22024, 8767, 25185, 1990, 1920, 3154, 1927, 4423, 9919, 18, 2052, 3533, 4952, 43, 2796, 1956, 14425, 3508, 4207, 2900, 16, 43, 4207, 3595, 2037, 1920, 4101, 6865, 3031, 1927, 1920, 28868, 2074, 26553, 2213, 18, 3], "antigen": ["NPDPNANPNVDPN"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human Fab, P2S-2E9 (IGHV2/IGLV2-Lambda), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the host cell membrane by interacting with host receptors, initiating infection and mediating fusion of viral and cellular membranes. The antibody is designed as a broadly neutralizing antibody targeting the outer face of the receptor-binding domain (RBD), capable of neutralizing diverse SARS-CoV-2 variants including omicron subvariants. Can you generate its HCDRs?", "target_protein": "ITLKESGPTLVKPTQTLTLTCTFSVGWIRQPPGKALEWLALRYSPSLKSRLTITKDTSKNQVVLTMTNMDPVDTATYYCWGQGTLVTVSSAGFSLSTSGVGIYWDDDKARHRIGYIFDY", "metadata": {"pdb_id": "7xsa", "light_chain_seq": "ALTQPASVSGSPGQSITISCTGTSSDVGDFNYVSWYQQHPGKAPKLMIYDVTKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYCCSSYTTSSISFGGGTKLTVLGQ", "cdrh1_seq": "GFSLSTSGVG", "cdrh2_seq": "IYWDDDK", "cdrh3_seq": "ARHRIGYIFDY", "cdrl1_seq": "SSDVGDFNY", "cdrl2_seq": "DVT", "cdrl3_seq": "SSYTTSSIS", "cdrh1_pos": "[24, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[23, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7xsa", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "P2S-2E9", "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGLV2", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "broad and potent neutralizing activity against all SARS-CoV-2 variants tested, including omicron"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 6914, 16, 7535, 1036, 17, 11416, 1026, 12, 20733, 15755, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 16, 12410, 2909, 1930, 10239, 5289, 1927, 4324, 1930, 3689, 5726, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 7642, 6171, 1927, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 7131, 1927, 12130, 6445, 20466, 17, 6083, 17, 22, 4936, 2710, 7254, 1935, 2830, 2316, 19313, 19196, 1036, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCG"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human Fab, abN48 (IGHV1/IGLV5-Lambda), targeting a peptide from the N-terminus of C-X-C chemokine receptor type 2 (CXCR2). CXCR2 is a receptor for interleukin-8 and other chemokines that activates neutrophils and mediates neutrophil chemotaxis to sites of tissue injury and inflammation. The antibody is designed to block IL-8-induced neutrophil chemotaxis and provide protection in inflammatory disease models by competing with the natural IL-8 ligand for binding to the CXCR2 N-terminus, thereby inhibiting neutrophil migration and inducing CXCR2 internalization. Please generate the HCDRs for this antibody.", "target_protein": "QLVQSGAEVKKPGSSVKVSCKASISWVRQAPGQGPEWMGWNYAQKFQGRVTMTRDTSISTAYMELSRLRPDDTAVYYCWGQGTLVTVSSAGGTLSSYAINPNSGGTASGYCSSTSCYDY", "metadata": {"pdb_id": "6kvf", "light_chain_seq": "VLTQPSSLSASPGASVSLTCTLRSGINVGAYRIYWYQQKPGSPPQFLLRYKSDSDKQQGSGVPSRFSGSRDASANAGILLISGLRSEDEADYYCAIWHSSAWVFGGGTQLTVLGG", "cdrh1_seq": "GGTLSSYA", "cdrh2_seq": "INPNSGGT", "cdrh3_seq": "ASGYCSSTSCYDY", "cdrl1_seq": "SGINVGAYR", "cdrl2_seq": "YKSDSDK", "cdrl3_seq": "AIWHSSAWV", "cdrh1_pos": "[23, 30]", "cdrh2_pos": "[48, 55]", "cdrh3_pos": "[94, 106]", "cdrl1_pos": "[23, 31]", "cdrl2_pos": "[49, 55]", "cdrl3_pos": "[94, 102]", "cdrh3_split": "val", "cdrh3_cluster": "6kvf", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "abN48", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV5", "is_engineered": false, "target_antigen": "C-X-C chemokine receptor type 2, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "block neutrophil chemotaxis and protect mice in an EAE model"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 4456, 6301, 12, 20733, 7390, 19, 28961, 1020, 1015, 17, 18279, 13, 16, 5133, 43, 4207, 2037, 1920, 56, 17, 7822, 1927, 45, 17, 66, 17, 45, 11673, 3148, 2601, 22, 12, 30353, 13, 18, 30353, 1977, 43, 3148, 1958, 9198, 17, 28, 1930, 2303, 12370, 1988, 9094, 8508, 1930, 10412, 9460, 16884, 1942, 3402, 1927, 2960, 4047, 1930, 4531, 18, 1920, 3533, 1977, 4609, 1942, 3367, 2614, 17, 28, 17, 2719, 9460, 16884, 1930, 3394, 6202, 1922, 3769, 2573, 3130, 2007, 11743, 1956, 1920, 4613, 2614, 17, 28, 5207, 1958, 2743, 1942, 1920, 30353, 56, 17, 7822, 16, 6113, 7918, 9460, 5049, 1930, 7834, 30353, 12071, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["FW"]} {"modality_type": "antibody", "text": "What would be the HCDR sequences of an antibody with the following function: A murine Fv (IGHV3/IGKV4-Kappa) targeting the voltage-gated potassium channel (KvAP) of Aeropyrum pernix. The voltage-gated potassium channel mediates voltage-dependent potassium ion permeability by assuming open or closed conformations in response to membrane voltage, forming a potassium-selective channel through which ions pass according to their electrochemical gradient. This antibody is intended as a structural tool to stabilize the channel for crystallographic analysis of voltage-sensing mechanisms.", "target_protein": "DVQLQESGPGLVKPSQSLSLTCTVTWNWIRQFPGNKLEWMGYSYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYFCWGQGTSVTVGYSITNNYAINYSGTTVRGYDYFAMDY", "metadata": {"pdb_id": "2a0l", "light_chain_seq": "QIVLTQSPAIMSASLGDRVTMTCTASSSVSSSYLHWYQQKPGSSPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSMEAEDAATYYCHQFHRSLTFGSGTKLE", "cdrh1_seq": "GYSITNNYA", "cdrh2_seq": "INYSGTT", "cdrh3_seq": "VRGYDYFAMDY", "cdrl1_seq": "SSVSSSY", "cdrl2_seq": "STS", "cdrl3_seq": "HQFHRSLT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "1ors", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fv", "heavy_subclass": "IGHV3", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Voltage-gated potassium channel, Aeropyrum pernix", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "structures of the voltage-dependent K+ channel KvAP, in complex with monoclonal Fv fragments"}}}, "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 11417, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1920, 6889, 17, 12336, 9057, 4999, 12, 10674, 2026, 13, 1927, 6049, 13518, 1989, 2079, 8635, 1039, 18, 1920, 6889, 17, 12336, 9057, 4999, 10412, 6889, 17, 3100, 9057, 4755, 8828, 2007, 10511, 4437, 2014, 8047, 12526, 1922, 2644, 1942, 3260, 6889, 16, 7402, 43, 9057, 17, 5328, 4999, 2596, 2154, 6982, 4675, 3147, 1942, 2310, 13197, 6494, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 1920, 4999, 1958, 17832, 2333, 1927, 6889, 17, 9306, 3531, 18, 3], "antigen": ["HPLVELGVSYAALLSVIVVVVEYTMQLSGEYLVRLYLVDLILVIILWADYAYRAYKSGDPAGYVKKTLYEIPALVPAGLLALIEGHLAGLGLFRLVRLLRFLRILLIISRGSKFLSAIADAADKIRFYHLFGAVMLTVLYGAFAIYIVEYPDPNSSIKSVFDALWWAVVTATTVGYGDVVPATPIGKVIGIAVMLTGISALTLLIGTVSNMFQK"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A human Fab, 16.a.26 (IGHV1/IGKV1-Kappa), targeting the Hemagglutinin of Influenza A virus (H3N2). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for membrane fusion via the HA2 subunit. The antibody is designed as a broadly neutralizing antibody capable of neutralizing diverse group 1 and group 2 influenza A virus subtypes, binding within the hemagglutinin stem.", "target_protein": "QVQLVQSGPEVKKPGASVKVSCKASISWVRQAPGQGLEWLGWNYAQKFQGRVTMTTDTSTSTASMELRSLRSDDTAVYYCWGQGTLVTVSSAGYSFSRYGISGYTGNTARDKKQGEVVLPAASFRWFAP", "metadata": {"pdb_id": "5k9q", "light_chain_seq": "DIQMTQSPVSLSASVGDRVTITCRASQSIGKFLNWYQQKPGRAPKLLIYYASNLETGGPSRFSGRGSETEFSLTISSLQPEDFATYYCQQSNNVPHTFGQGTKLEIKRT", "cdrh1_seq": "GYSFSRYG", "cdrh2_seq": "ISGYTGNT", "cdrh3_seq": "ARDKKQGEVVLPAASFRWFAP", "cdrl1_seq": "QSIGKF", "cdrl2_seq": "YAS", "cdrl3_seq": "QQSNNVPHT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 116]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5k9q", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "16.a.26", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus (strain A/Hong Kong/1/1968 H3N2)", "target_domain": "hemagglutinin stem", "functional_role": "neutralizing", "evidence_quote": "capable of neutralizing diverse subtypes of group 1 and group 2 influenza A viruses"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 2616, 6914, 16, 2641, 18, 43, 18, 3179, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 12, 25234, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 3260, 5289, 3454, 1920, 2118, 1028, 5903, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 7131, 1927, 12130, 6445, 2210, 21, 1930, 2210, 22, 7108, 43, 3413, 8160, 16, 2743, 2651, 1920, 26141, 4402, 18, 3], "antigen": ["FIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRF", "STATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIESRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEK"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A human Fab, UT14 (IGHV3/IGKV3-Kappa), targeting the engineered Hemagglutinin of Influenza A virus (A/Singapore/INFIMH-16-0019/2016, H3N2). Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for penetration into the cell cytoplasm by mediating membrane fusion. This antibody forms a complex with the Hemagglutinin head domain and recognizes the HA trimer interface, binding to both group 1 and 2 HAs. Generate the corresponding HCDRs.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCATSIHWVRQAPGKGLGWVAMYYADSVRGRFTISRDNSKNTLSLQMNSLRTEDTAVYYCWGQGTLVTVSSGFTFSSYGISFDGSKTAKERDRDGYNEGIYDY", "metadata": {"pdb_id": "8uzc", "light_chain_seq": "EIVMTQSPATLSLSPGERATLSCRASGFYLAWYQQKPGQAPRLLIYDTSNRATGIPARFSGRGSGTDFTLTINSLEPEDFAVYYCQQRYNWPITFGQGTRLEIK", "cdrh1_seq": "GFTFSSYG", "cdrh2_seq": "ISFDGSKT", "cdrh3_seq": "AKERDRDGYNEGIYDY", "cdrl1_seq": "GFY", "cdrl2_seq": "DTS", "cdrl3_seq": "QQRYNWPIT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[26, 28]", "cdrl2_pos": "[46, 48]", "cdrl3_pos": "[85, 93]", "cdrh3_split": "val", "cdrh3_cluster": "8uzc", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "UT14", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": null, "functional_role": "unknown", "evidence_quote": "highly abundant monoclonal antibody that binds to both group 1 and 2 HAs"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 11112, 3745, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 26141, 1927, 7108, 43, 3413, 12, 43, 19, 21561, 19, 2122, 1980, 1023, 17, 2641, 17, 3472, 1026, 19, 4759, 16, 25234, 13, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 12006, 2460, 1920, 2024, 5239, 2007, 10239, 3260, 5289, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 26141, 4469, 3418, 1930, 16197, 1920, 2118, 20085, 6854, 16, 2743, 1942, 2321, 2210, 21, 1930, 22, 2258, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["ICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWTGVTQNGTSSACIRGSSSSFFSRLNWLTHLNYTYPALNVTMPNKEQFDKLYIWGVHHPGSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSKSSIMRSDAPIGKCK"]} {"modality_type": "antibody", "text": "A human Fab (IGHV4/IGKV3-Kappa) targeting the Hemagglutinin HA1 chain of Influenza A virus (H5N1). Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and internalization, and functions as a class I viral fusion protein responsible for penetration of the virus into the cell cytoplasm. This antibody forms a complex with the Hemagglutinin HA1 chain. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "MQLQESGPGLVKPSGTLSLTCAVSWSWVRQSPGKGLEWIGEYYNPSLKSRLTISVDKSKNQFSLKLTSVTAADTAVYFCWGQGTTVTVGGSISNSHWIYHSGSTARGLGWEQGGYRAFDM", "metadata": {"pdb_id": "9mq7", "light_chain_seq": "EIVMTQSPATLSVSPGERVTLSCRASQSVGSSLAWYQQKPGQAPRLLIYAASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQHYNWPPLTFGGGTKVEI", "cdrh1_seq": "GGSISNSHW", "cdrh2_seq": "IYHSGST", "cdrh3_seq": "ARGLGWEQGGYRAFDM", "cdrl1_seq": "QSVGSS", "cdrl2_seq": "AAS", "cdrl3_seq": "QQHYNWPPLT", "cdrh1_pos": "[24, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "9mq7", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Hemagglutinin HA1 chain, Influenza A virus", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 43, 2616, 6914, 12, 20733, 1020, 1006, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 26141, 2118, 1009, 4659, 1927, 7108, 43, 3413, 12, 20128, 13, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 12071, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 12006, 1927, 1920, 3413, 2460, 1920, 2024, 5239, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 26141, 2118, 1009, 4659, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["ICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPMCDEFIRVPEWSYIVERANPANDLCFPGSLNDYEELKHMLSRINHFEKIQIIPKSSWPNHETSLGVSAACPYQGAPSFFRNVVWLIKKNDAYPTIKISYNNTNREDLLILWGIHHSNNAEEQTNLYKNPITYISVGTSTLNQRLAPKIATRSQVNGQRGRMDFFWTILKPDDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSGVEYGHCNTKCQTPVGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLR"]} {"modality_type": "antibody", "text": "Output the HCDRs for an antibody that performs this function: A murine Fab, 7D11 (IGHV1/IGKV8-Kappa), targeting the Virion membrane protein M25 (L1 protein) of Vaccinia virus. The L1 protein is a component of the entry fusion complex, which mediates entry of the virion core into the host cytoplasm through lipid mixing and pore formation. The antibody is designed as a neutralizing antibody that recognizes a conformational epitope formed by two loops held together by a disulfide bond.", "target_protein": "QVQLQQSGAELAKPGASVKMSCKASMHWVKQRPGQGLEWIGYEYNQKFKDKATLTADKSSSTVYMQLSSLTSEDSAVYYCWGQGTLVTVSAAGYTFTRYWINPSTGYTARTTVDGYDFAY", "metadata": {"pdb_id": "2i9l", "light_chain_seq": "DMVMSQSPSSLAVSAGEKVSMSCKSSQTLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLWTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTRYW", "cdrh2_seq": "INPSTGYT", "cdrh3_seq": "ARTTVDGYDFAY", "cdrl1_seq": "QTLLNSRTRKNY", "cdrl2_seq": "WAS", "cdrl3_seq": "KQSYNLWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 101]", "cdrh3_split": "val", "cdrh3_cluster": "2i9l", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "7D11", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV8", "is_engineered": false, "target_antigen": "Virion membrane protein M25 (L1 protein), Vaccinia virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody against the poxvirus L1 protein"}}}, "tokenized_instruction": [2, 6647, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 17436, 2052, 2347, 30, 43, 7135, 6914, 16, 15868, 3242, 12, 20733, 7390, 19, 7021, 1040, 1020, 1025, 17, 12093, 13, 16, 5133, 1920, 19230, 3260, 2213, 6056, 1015, 12, 7554, 2213, 13, 1927, 24331, 3413, 18, 1920, 7554, 2213, 1977, 43, 4594, 1927, 1920, 6904, 5289, 2796, 16, 2154, 10412, 6904, 1927, 1920, 19230, 4728, 2460, 1920, 4423, 5239, 2596, 4486, 10845, 1930, 8554, 3337, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 16197, 43, 8523, 10095, 5333, 2007, 2288, 11109, 9865, 4084, 2007, 43, 11830, 5403, 18, 3], "antigen": ["AASIQTTVNTLSERISSKLEQEANASAQTKCDIEIGNFYIRQNHGCNLTVKNMCSADADAQLDAVLSAATETYSGLTPEQKAYVPAMFTAALNIQTSVNTVVRDFENYVKQTCNSSAVVDNKLKIQNVIIDECYGAPGSPTNLEFINTGSSKGNCAIKALMQLTTKATTQIAP"]} {"modality_type": "antibody", "text": "A murine Fab, G2 (IGHV1/IGKV3-Kappa), targeting the Spike glycoprotein of Middle East respiratory syndrome-related coronavirus. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptor DPP4 to mediate viral entry, and mediates fusion of the virion and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that prevents DPP4 binding to the trimeric spike through an indirect mechanism dependent on the intact trimeric conformation, binding within the S1 N-terminal domain (S1-NTD). The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "QVQLQQSGGELVKPGASVKLSCKTSISWLKQKPGQSLEWIAWEYNQKFTGKAQVTVDTSSSTAYMQFSSLTTEDSAIYYCWGQGTSVTVGFTFSSSYIYAGTGGTARGGSSFAMDY", "metadata": {"pdb_id": "6pz8", "light_chain_seq": "QLVLTQSPASLAVSLGQRATISCRASESSFMNWFQQKPGQPPKLLIHTASNQGSGVPARFSGSGSGTDFSLNIHPVEDDDTAMYFCQQSEEVPLTFGAGTKLE", "cdrh1_seq": "GFTFSSSY", "cdrh2_seq": "IYAGTGGT", "cdrh3_seq": "ARGGSSFAMDY", "cdrl1_seq": "ESSF", "cdrl2_seq": "TAS", "cdrl3_seq": "QQSEEVPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "6pxh", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "G2", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Middle East respiratory syndrome-related coronavirus", "target_domain": "S1 N-terminal domain (S1-NTD)", "functional_role": "neutralizing", "evidence_quote": "neutralizes MERS-CoV by interfering with binding to host receptor dipeptidyl peptidase-4 (DPP4)"}}}, "tokenized_instruction": [2, 43, 7135, 6914, 16, 9616, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 5576, 10319, 5481, 4741, 17, 2712, 5548, 10703, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 3148, 16423, 1006, 1942, 8265, 4324, 6904, 16, 1930, 10412, 5289, 1927, 1920, 19230, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 10299, 16423, 1006, 2743, 1942, 1920, 29177, 10429, 2596, 1925, 6354, 2856, 3100, 1990, 1920, 6718, 29177, 7748, 16, 2743, 2651, 1920, 4062, 56, 17, 4262, 3418, 12, 4062, 17, 22078, 13, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["YVDVGPDSVKSACIEVDIQQTFFDKTWPRPIDVSKADGIIYPQGRTYSNITITYQGLFPYQGDHGDMYVYSAGHATGTTPQKLFVANYSQDVKQFANGFVVRIGAAANSTGTVIISPSTSATIRKIYPAFMLGSSVGNFSDGKMGRFFNHTLVLLPDGCGTLLRAFYCILEPRSGNHCPAGNSYTSFATYHTPATDCSDGNYNRNASLNSFKEYFNLRNCTFMYTYNITEDEILEWFGITQTAQGVHLFSSRYVDLYGGNMFQFATLPVYDTIKYYSIIPHSIRSIQSDRKAWAAFYVYKLQPLTFLLDFSVDGYIRRAIDCGFNDLSQLHCSYESFDVESGVYSVSSFEAKPSGSVVEQAEDTKIASQLGNCVEYSLYGVSGRGVFQNCTAVGVRQQRFVYDAYQNLVGYYSDDGNYYCLRACVSVPVSVIYDKETKTHATLFGSVACEHISSTMSQYSRSTRSMLKRRDSTYGPLQTPVGCVLGLVNSSLFVEDCKLPLGQSLCALPDTPS"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, 857-2 (IGHV5/IGKV1-Kappa), targeting the Outer surface protein A of Borreliella burgdorferi. Outer surface protein A induces host cytokine release by monocyte cell lines via TLR2 and CD14 signaling. This antibody forms a complex with Outer surface protein A.", "target_protein": "EVQLVQSGEEVKKPGESLKISCKGSIGWVRQMPGKGLEWMGIRYSPSFQGQVTISADKSISTVYLQWSSLKASDTAMYYCWGQGTLVTVSSAGYKFSSYWIFPGDSDKARHITTHTYRGFFDF", "metadata": {"pdb_id": "8tuz", "light_chain_seq": "QLTQSPSSLSASVGDRVTITCRASQDISSALAWYQQKPGKAPKLLIYDVSSLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQFNGYPHRLTFGGGTKVEIKRT", "cdrh1_seq": "GYKFSSYW", "cdrh2_seq": "IFPGDSDK", "cdrh3_seq": "ARHITTHTYRGFFDF", "cdrl1_seq": "QDISSA", "cdrl2_seq": "DVS", "cdrl3_seq": "QQFNGYPHRLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8tuz", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Outer surface protein A, Borreliella burgdorferi", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 5140, 1027, 17, 22, 12, 20733, 1020, 1015, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 7642, 3154, 2213, 43, 1927, 27037, 19918, 24902, 18, 7642, 3154, 2213, 43, 6387, 4423, 6137, 4012, 2007, 12064, 2024, 3557, 3454, 15235, 1930, 13357, 3197, 18, 2052, 3533, 4952, 43, 2796, 1956, 7642, 3154, 2213, 43, 18, 3], "antigen": ["SLDEKNSVSVDLPGEMKVLVSKEKNKDGKYDLIATVDKLELKGTSDKNNGSGVLEGVKADKSKVKLTISDDLGQTTLEVFKEDGKTLVSKKVTSKDKSSTEEKFNEKGEVSEKIITRADGTRLEYTGIKSDGSGKAKEVLKGYVLEGTLTAEKTTLVVKEGTVTLSKNISKSGEVSVELNDTDSSAATKKTAAWNSGTSTLTITVNSKKTKDLVFTKENTITVQQYDSNGTKLEGSAVEITKLDEIKNALK"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A human Fab (IGHV1/IGKV2D-Kappa) targeting the C-terminus of Amyloid-beta A4 protein (A\u03b240) from Homo sapiens. Amyloid-beta peptides are lipophilic metal chelators that bind transient metals such as copper, zinc, and iron, and promote tau aggregation and neuronal dysfunction. The antibody is designed to bind the C-terminal epitope of soluble A\u03b240 to elevate circulating A\u03b2 levels and reduce amyloid burden in the brain parenchyma.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASIHWVRQAPGQGLEWMGRKYAPRLQDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCWGQGTTVTVSSAGYYTEAYYIDPATGNTASLYSLPVY", "metadata": {"pdb_id": "3u0t", "light_chain_seq": "DVVMTQSPLSLPVTLGQPASISCKSSQSLLYSDAKTYLNWFQQRPGQSPRRLIYQISRLDPGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCLQGTHYPVLFGQGTRLEIKRT", "cdrh1_seq": "GYYTEAYY", "cdrh2_seq": "IDPATGNT", "cdrh3_seq": "ASLYSLPVY", "cdrl1_seq": "QSLLYSDAKTY", "cdrl2_seq": "QIS", "cdrl3_seq": "LQGTHYPVL", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 104]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "3u0t", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV2D", "is_engineered": false, "target_antigen": "Amyloid-beta A4 protein, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "ponezumab greatly elevates plasma A\u03b240 levels and reduces hippocampal amyloid load"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 15755, 1007, 17, 12093, 13, 5133, 1920, 45, 17, 7822, 1927, 8186, 17, 4666, 16440, 2213, 12, 27922, 13, 2037, 16350, 27974, 18, 8186, 17, 4666, 5320, 2032, 21140, 6048, 28914, 1036, 1988, 4566, 6809, 11570, 2427, 1966, 9541, 16, 7997, 16, 1930, 5680, 16, 1930, 5527, 7462, 7883, 1930, 5121, 5273, 18, 1920, 3533, 1977, 4609, 1942, 4566, 1920, 45, 17, 4262, 10095, 1927, 6622, 27922, 1942, 27565, 7396, 6504, 2428, 1930, 4412, 8186, 6700, 1922, 1920, 3068, 15214, 18, 3], "antigen": ["AIIGLMVGGVV"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab, ZWC6 (IGHV3/IGKV3-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (Delta variant). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that blocks spike protein binding to ACE2 receptor.", "target_protein": "VQLVESGGGVVQPGTSLRLSCAASMYWVRQAPGKGLDWVAIYYADSVKGRFTISRDNSKDTLYLQMHSLRPEDTAVYYCWGQGTLVTVSGFSFSHYVISFDGSSQAIHGGTYYYDKNILA", "metadata": {"pdb_id": "7wwm", "light_chain_seq": "IRMTQSPPTLSLSPGERATLSCRASQSVTNYLVWYQQKPGQAPRLLIYDTFNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPTFGQGTKVDI", "cdrh1_seq": "GFSFSHYV", "cdrh2_seq": "ISFDGSSQ", "cdrh3_seq": "AIHGGTYYYDKNILA", "cdrl1_seq": "QSVTNY", "cdrl2_seq": "DTF", "cdrl3_seq": "QQRSNWPPT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 109]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "7wwm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ZWC6", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "blocked S protein binding to ACE2"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 16, 21933, 24304, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 9649, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 10429, 2213, 2743, 1942, 8298, 1028, 3148, 18, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFVYSSANNCTFEYVSKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSALGKLQNVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A murine Fab, Fab7G7 (IGHV1/IGKV6-Kappa), targeting the engineered Proprotein convertase subtilisin/kexin type 9 of Homo sapiens. PCSK9 regulates plasma LDL cholesterol levels by promoting the degradation of liver LDL receptors through binding to the EGF(A) domain of LDLR. The antibody is designed to inhibit PCSK9 binding to LDLR, thereby preventing LDLR degradation and lowering plasma LDL cholesterol.", "target_protein": "QVQLKQSGAELVRPGASVKLSCKASINWLKKRPGQGLEWIARYYNENFKDKATLTAEKSSSNVYMQLSSLTSEDSAVYFCWGTGTTVTVSSAGYIFTDYYIYPGSGHTARENFYGSSYVDWYFDV", "metadata": {"pdb_id": "5vlp", "light_chain_seq": "DIVMTQSQKFMSTSGGDRVSITCKTSQNVGTAVAWFQQKPGQSPKLLIYSASNRYTGVSDRFTGSGSGTEFIFTISYAQSEDLADYFCHQYSSYPLTFGAGTKLELKRA", "cdrh1_seq": "GYIFTDYY", "cdrh2_seq": "IYPGSGHT", "cdrh3_seq": "ARENFYGSSYVDWYFDV", "cdrl1_seq": "QNVGTA", "cdrl2_seq": "SAS", "cdrl3_seq": "HQYSSYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7bh8", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Fab7G7", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Proprotein convertase subtilisin/kexin type 9, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "Antibodies that inhibit PCSK9 binding to the EGF(A) domain of the LDLR are effective in lowering LDL-c"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 6914, 1027, 1029, 1027, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 11091, 12031, 7229, 1921, 14450, 2051, 14745, 1921, 19, 3364, 10960, 2601, 29, 1927, 16350, 27974, 18, 26601, 7014, 3582, 8017, 5463, 2428, 2007, 7356, 1920, 4877, 1927, 3568, 8017, 4086, 2596, 2743, 1942, 1920, 4451, 12, 43, 13, 3418, 1927, 20944, 18, 1920, 3533, 1977, 4609, 1942, 2875, 26601, 2743, 1942, 20944, 16, 6113, 8444, 20944, 4877, 1930, 11187, 3582, 8017, 5463, 18, 3], "antigen": ["TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPEQVTVACEEGWTLTGCSALPSHVLGAYAVDNTCVVRSRAVTAVAICCRSR"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A rhesus macaque Fab, 5C8 (IGHV4/IGKV1-Kappa), targeting the prefusion Fusion glycoprotein F0 of Nipah virus. The Fusion glycoprotein F0 is a class I viral fusion protein that undergoes conformational transitions from prefusion to postfusion states, with heptad repeat regions forming a trimer-of-hairpins structure that drives fusion of viral and cellular membranes. The antibody is designed as a broadly neutralizing antibody that stabilizes the prefusion F-trimer conformation to prevent membrane fusion.", "target_protein": "QVQLQESGPGVVKPSETLSLTCAVSWSWIRQPPGKGLEWIGYNYNPSLKSRVTISKDTSKNQFSLNLSSLTAADTAVYYCWGPGVLVTVGGSISDSYRIYGSSTSTVRVVQYLEWFVDLIEVNWFDV", "metadata": {"pdb_id": "9uaa", "light_chain_seq": "DIQLTQSPSSLSASVGDTVTITCQASQGIGNNLHWYQQKPGKAPKLLIYRASSLQSGIPSRFSGSGSGTDYTLTISSLQPEDFAYYCQQGYSYPFTFGPGTKVDIK", "cdrh1_seq": "GGSISDSYR", "cdrh2_seq": "IYGSSTST", "cdrh3_seq": "VRVVQYLEWFVDLIEVNWFDV", "cdrl1_seq": "QGIGNN", "cdrl2_seq": "RAS", "cdrl3_seq": "QQGYSYPFT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 58]", "cdrh3_pos": "[97, 117]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "8xnh", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "5C8", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Fusion glycoprotein F0, Nipah virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibody; cross-neutralization against HNVs; confers robust protection against lethal Nipah virus challenge"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 16996, 20533, 6914, 16, 9083, 1025, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 9328, 2670, 5289, 11424, 17930, 1927, 18786, 5945, 3413, 18, 1920, 5289, 11424, 17930, 1977, 43, 2921, 51, 4324, 5289, 2213, 1988, 14928, 8523, 10673, 2037, 9328, 2670, 1942, 2753, 9049, 4376, 16, 1956, 20662, 2015, 6865, 3451, 7402, 43, 20085, 17, 1927, 17, 14565, 1036, 3170, 1988, 15435, 5289, 1927, 4324, 1930, 3689, 5726, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1988, 19658, 1920, 9328, 2670, 48, 17, 20085, 7748, 1942, 4625, 3260, 5289, 18, 3], "antigen": ["ILHYEKLSKIGLVKGVTRKYKIKSNPLTKDIVIKMIPNVSNMSQCTGSVMENYKTRLNGILTPIKGALEIYKNNTHDLGVIMAGVAIGIATAAQITAGVALYEAMKNADNINKLKSSIESTNEAVVKLQETAEKTVYVLTALQDYINTNLVPTIDKISCKQTELSLDLALSKYLSDLLFVFGPNLQDPVSNSMTIQAISQAFGGNYETLLRTLGYATEDFDDLLESDSITGQIIYVDLSSYYIIVRVYFPILTEIQQAYIQELLPVSFNNDNSEWISIVPNFILVRNTLISNIEIGFCLITKRSVICNQDYATPMTNNMRECLTGSTEKCPRELVVSSHVPRFALSNGVLFANCISVTCQCQTTGRAISQSGEQTLLMIDNTTCPTAVLGNVIISLGKYLGSVNYNSEGIAIGPPVFTDKVDISSQISSMNQSLQQSK"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A human Fab, R12 (IGHV1/IGLV5-Lambda), targeting the Gn glycoprotein of Rift valley fever virus. The Gn glycoprotein is a class II fusion protein that attaches the virion to the host cell receptor CD209/DC-SIGN and promotes fusion of membranes with the late endosome after endocytosis. The antibody is designed as a neutralizing antibody that blocks virion attachment to host cells by interfering with Gn binding.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKVSMHWVRQAPGKGLEWMGGIYAQKFQGRVTMTEDTSTDTAYMELSSLRSEDTAVYYCWGQGTLVTVSSAGYTLTELSFDREDGETAIDPIRYNWNYGDY", "metadata": {"pdb_id": "6iek", "light_chain_seq": "PVLTQPPSSSASPGESARLTCTLPSDISVSSYNIYWYQQKPGSPPRFLLYYYSDSDKGQGSGVPSRFSGSKDASDNTGILLISGLQSEDEADYYCMIWPSNAWVFGGGTKLTVLGQ", "cdrh1_seq": "GYTLTELS", "cdrh2_seq": "FDREDGET", "cdrh3_seq": "AIDPIRYNWNYGDY", "cdrl1_seq": "SDISVSSYN", "cdrl2_seq": "YYSDSDK", "cdrl3_seq": "MIWPSNAWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 56]", "cdrl3_pos": "[95, 103]", "cdrh3_split": "val", "cdrh3_cluster": "6iek", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "R12", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV5", "is_engineered": false, "target_antigen": "Envelopment polyprotein (Gn), Rift valley fever virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "Gn monoclonal antibodies interfere with soluble Gn binding to cells and prevent infection by blocking the attachment of virions to host cells"}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 12041, 1028, 12, 20733, 7390, 19, 28961, 1020, 1015, 17, 18279, 13, 16, 5133, 1920, 9005, 11424, 1927, 12424, 1031, 19469, 9087, 3413, 18, 1920, 9005, 11424, 1977, 43, 2921, 2890, 5289, 2213, 1988, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3148, 16494, 1026, 19, 5330, 17, 2105, 1930, 7383, 5289, 1927, 5726, 1956, 1920, 5058, 22321, 2256, 11914, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 19230, 8576, 1942, 4423, 2094, 2007, 13369, 1956, 9005, 2743, 18, 3], "antigen": ["EDPHLRNRPGKGHNYIDGMTQEDATCKPVTYAGACSSFDVLLEKGKFPLFQSYAHHRTLLEAVHDTIIAKADPPSCDLQSAHGNPCMKEKLVMKTHCPNDYQSAHYLNNDGKMASVKCPPKYELTEDCNFCRQMTGASLKKGSYPLQDLFCQSSEDDGSKLKTKMKGVCEVGVQALKKCDGQLSTAHEVVPFAVFKNSKKVYLDKLDLKTEENLLPDSFVCFEHKELKSFDISQCPKIGGHGSKKCTGDAAFCSAYECTAQYANAYCSHANGSGIVQIQVSGVWKKPLCVGYERVVVKREL"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (Omicron variant). The Spike glycoprotein attaches the virion to the host cell membrane by interacting with the ACE2 receptor, initiating infection. The antibody is designed as a neutralizing antibody targeting a proteoglycan epitope on the outer face of the Receptor-binding domain (RBD), which remains accessible and conserved across the Omicron variant despite extensive mutations.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7yad", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVE", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "S309 retaining its neutralizing activity against Omicron"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 7254, 1935, 2830, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 1920, 8298, 1028, 3148, 16, 12410, 2909, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 43, 25445, 10095, 1990, 1920, 7642, 6171, 1927, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 2154, 4497, 10551, 1930, 5305, 3436, 1920, 7254, 1935, 2830, 6031, 4281, 6475, 3527, 18, 3], "antigen": ["PNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKK"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab, MF3958 (IGHV1/IGKV1-Kappa), targeting the Receptor tyrosine-protein kinase erbB-2 (HER2) of Homo sapiens. HER2 is a protein tyrosine kinase that regulates cell surface receptor complexes and is essential for neuregulin-receptor signaling and microtubule stabilization. The antibody is designed as part of a bispecific IgG1 to inhibit HER3 signaling through HER2-guided ligand blockade, preventing heregulin-mediated PI3K/Akt pathway activation in HER2-driven cancers.", "target_protein": "QVQLVQSGAEVKKPGASVKLSCKASINWVRQAPGQGLEWIGRSYAQKFQGRATLTADESTSTAYMELSSLRSEDTAVYFCWGQGTLVTVSSAGYTFTAYYIYPGSGYTARPPVYYDSAWFAY", "metadata": {"pdb_id": "5o4g", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPTFGQGTKVEIKRT", "cdrh1_seq": "GYTFTAYY", "cdrh2_seq": "IYPGSGYT", "cdrh3_seq": "ARPPVYYDSAWFAY", "cdrl1_seq": "QSISSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSYSTPPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6bzy", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "MF3958", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Receptor tyrosine-protein kinase erbB-2 (HER2), Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "bispecific IgG1 potently inhibits the HRG/HER3 pathway via a dock & block mechanism"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 8168, 6021, 7532, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 3148, 6941, 17, 2213, 4016, 11954, 17, 22, 12, 9162, 13, 1927, 16350, 27974, 18, 9162, 1977, 43, 2213, 6941, 4016, 1988, 7014, 2024, 3154, 3148, 5048, 1930, 1977, 4415, 1958, 2974, 6541, 3392, 17, 3148, 3197, 1930, 10544, 10281, 18, 1920, 3533, 1977, 4609, 1966, 3131, 1927, 43, 7266, 10231, 15368, 1942, 2875, 3656, 1010, 3197, 2596, 9162, 17, 9663, 5207, 9847, 16, 8444, 3410, 11056, 7782, 17, 3434, 7734, 19, 5496, 3374, 2936, 1922, 9162, 17, 6446, 5717, 18, 3], "antigen": ["TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCH"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab, H7.200 (IGHV4/IGKV1-Kappa), targeting the engineered Hemagglutinin of Influenza A virus (H7N9). Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for membrane fusion. The antibody is designed as a pan-H7 protective antibody that recognizes a conserved epitope in the HA head domain trimer interface.", "target_protein": "QVQLVESGPGLVKPSQTLSLTCTVSWSWIRQPAGKGLEWIGRNYNPSLKSRVTISLDTSKNQFSLKLSSVTAADTAVYYCWGKGTLVTVSSAGGSINSSHSFIYSTGNSARESLWNPDYYYYMDV", "metadata": {"pdb_id": "6uig", "light_chain_seq": "DIVMTQSPSSLSASVGDRVTITCRASQSFSSHLNWYQQKPGRAPDLLIYAASSLHSGVPSRFSGSGSGTDFTLTISSLQPEDFAVYYCQQSYSVPYTFGQGTKLQIKRT", "cdrh1_seq": "GGSINSSHSF", "cdrh2_seq": "IYSTGNS", "cdrh3_seq": "ARESLWNPDYYYYMDV", "cdrl1_seq": "QSFSSH", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSYSVPYT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6uig", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "H7.200", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": null, "functional_role": "other", "evidence_quote": "pan-H7, non-neutralizing, protective human Ab"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 16754, 18, 2191, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 26141, 1927, 7108, 43, 3413, 12, 16754, 28955, 13, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 3797, 17, 16754, 6337, 3533, 1988, 16197, 43, 5305, 10095, 1922, 1920, 2118, 4469, 3418, 20085, 6854, 18, 3], "antigen": ["TVERTNIPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKEAMGFTYSGIRTNGATSACRRSGSSFYAEMKWLLSNTDNAAFPQMTKSYKNTRKSPALIVWGIHHSVSTAEQTKLYGSGNKLVTVGSSNYQQSFVPSPGARPQVNGLSGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGIQSGVQVDANCEGDCYHSGGTIISNLPFQNIDSRAVGKCPRYV"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A murine Fab (IGHV1/IGKV16-Kappa) targeting the nitric oxide reductase complex, composed of subunits B and C from Pseudomonas aeruginosa. Nitric oxide reductase is a component of the anaerobic respiratory chain that catalyzes the reduction of nitric oxide to nitrous oxide and shows proton pump activity across the membrane in denitrifying bacterial cells. This antibody is intended as a structural tool to facilitate crystallographic characterization of the nitric oxide reductase complex. Please provide the HCDR sequences.", "target_protein": "EVQLQQSGTVLARPGASVKMSCKASMHWVKQRPGQGLEWIGASYNQKFKGKAKLTAVTSASTAYMELSSLTNEDSAVYYCWGQGTTVTVSSAGYSFTSYWVYPGNSDTSRSSLDGYYVKNWCFDV", "metadata": {"pdb_id": "3o0r", "light_chain_seq": "DIQMTQSPPYLAASPGETITINCRASKSIRKYLAWYQEKPGKTNKLLIYSGSTLQFGIPSRFSGSGSGTEFTLTISSLEPEDFAMYYCQQHNEYPLTFGAGTKLELKRA", "cdrh1_seq": "GYSFTSYW", "cdrh2_seq": "VYPGNSDT", "cdrh3_seq": "SRSSLDGYYVKNWCFDV", "cdrl1_seq": "KSIRKY", "cdrl2_seq": "SGS", "cdrl3_seq": "QQHNEYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3o0r", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV16", "is_engineered": false, "target_antigen": "Nitric oxide reductase subunits B and C, Pseudomonas aeruginosa", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "Crystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with antibody fragment"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 1016, 17, 12093, 13, 5133, 1920, 10233, 7491, 11386, 2796, 16, 7179, 1927, 6991, 44, 1930, 45, 2037, 13461, 10830, 18, 10233, 7491, 11386, 1977, 43, 4594, 1927, 1920, 12554, 5481, 4659, 1988, 17097, 1920, 3378, 1927, 10233, 7491, 1942, 8686, 1957, 7491, 1930, 3661, 8433, 8912, 2455, 3436, 1920, 3260, 1922, 26319, 7649, 4543, 2094, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 6628, 17832, 7285, 1927, 1920, 10233, 7491, 11386, 2796, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["FASQAVAKPYFVFALILFVGQILFGLIMGLQYVVGDFLFPAIPFNVARMVHTNLLIVWLLFGFMGAAYYLVPEESDCELYSPKLAWILFWVFAAAGVLTILGYLLVPYAGLARLTGNELWPTMGREFLEQPTISKAGIVIVALGFLFNVGMTVLRGRKTAISMVLMTGLIGLALLFLFSFYNPENLTRDKFYWWWVVHLWVEGVWELIMGAILAFVLVKITGVDREVIEKWLYVIIAMALISGIIGTGHHYFWIGVPGYWLWLGSVFSALEPLPFFAMVLFAFNTINRRRRDYPNRAVALWAMGTTVMAFLGAGVWGFMHTLAPVNYYTHGTQLTAAHGHMAFYGAYAMIVMTIISYAMPRLRGIGEAMDNRSQVLEMWGFWLMTVAMVFITLFLSAAGVLQVWLQRMPADGAAMTFMATQDQLAIFYWLREGAGVVFLIGLVAYLLSF", "FTKGMARNIYFGGSVFFILLFLALTYHTEKTLPERTNEAAMSAAVVRGKLVWEQNNCVGCHTLLGEGAYFAPELGNVVGRRGGEEGFNTFLQAWMKIQPLNVPGRRAMPQFHLSEGQVDDLAEFLKWSSKIDTNQWPPNKEG"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes during entry. This antibody forms a complex with the Spike glycoprotein within the Receptor-binding domain (RBD), used as a structural tool in a quaternary complex with DARPin SR16m and antibody CR3022 to enable cryo-EM structure determination. Generate the corresponding HCDRs.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "8dw3", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2409, 6904, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 11424, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 2251, 1966, 43, 4346, 5229, 1922, 43, 21920, 2796, 1956, 14574, 9512, 4581, 3672, 1035, 1930, 3533, 2345, 29906, 1028, 1942, 8675, 15822, 17, 2391, 3170, 7063, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["LCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A murine Fab, 8D3 (IGHV1/IGKV6-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 Delta variant. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor to initiate infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a broadly neutralizing antibody capable of cross-neutralizing multiple SARS-CoV-2 variants including Delta, Beta, and Kappa by competitively blocking ACE2 receptor binding. Please generate its HCDRs.", "target_protein": "EVQLQQSGPELVKPGASVKISCKTSMYWVKQSHGKSLEWIGGSYNQNFKGKATLTVDRSSSTAYMELRSLTSEDSAVYYCWGQGTSVTVSSAGYTFTEYTINPNIGDTARDGYPYYYALDH", "metadata": {"pdb_id": "7w9e", "light_chain_seq": "DIVMTQSQKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALIYSTSYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQYNSYPYTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTEYT", "cdrh2_seq": "INPNIGDT", "cdrh3_seq": "ARDGYPYYYALDH", "cdrl1_seq": "QNVGTN", "cdrl2_seq": "STS", "cdrl3_seq": "QQYNSYPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7w9e", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "8D3", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "potent cross-neutralization with IC50s against Delta, Beta, and Kappa being 7.6, 6.3, and 2.2 ng/mL"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 23865, 1010, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 9649, 6031, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1942, 11051, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 7131, 1927, 3567, 17, 12130, 3137, 20466, 17, 6083, 17, 22, 4936, 2710, 9649, 16, 4666, 16, 1930, 12093, 2007, 10362, 1954, 7472, 8298, 1028, 3148, 2743, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["QCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQNVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A murine Fab (IGHV1/IGKV1-Kappa) targeting the engineered Leukocidin E of Staphylococcus aureus. Leukocidin E is part of a bi-component leucotoxin that acts by forming pores in the membrane of target cells. The antibody is designed to neutralize the pore-forming activity of leukocidins as part of a multivalent mAbtyrin fusion construct for protection against S. aureus infection.", "target_protein": "QVQLQQSGAELMNPGASVKISCKSTIEWVKQRPGHGLEWMGENHNEKFKGKAIFTADASSNTAYMELSSLTSEDSAVYYCWGQGTLVTVSAAGYKFSSYWILPGSGSTARTISTATDWFAY", "metadata": {"pdb_id": "7t82", "light_chain_seq": "DVLMTQTPLSLPVSLGDQASISCRSSQTIVYSDGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRVSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKRT", "cdrh1_seq": "GYKFSSYW", "cdrh2_seq": "ILPGSGST", "cdrh3_seq": "ARTISTATDWFAY", "cdrl1_seq": "QTIVYSDGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQGSHVPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "7t82", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Leukocidin E, Staphylococcus aureus", "target_domain": null, "functional_role": "other", "evidence_quote": "neutralizes pore-forming leukocidins via fusion with anti-toxin centyrins"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11091, 5104, 2240, 22816, 47, 1927, 13452, 8849, 18, 5104, 2240, 22816, 47, 1977, 3131, 1927, 43, 2273, 17, 4594, 9906, 11140, 1988, 8016, 2007, 7402, 14711, 1922, 1920, 3260, 1927, 2758, 2094, 18, 1920, 3533, 1977, 4609, 1942, 25885, 1920, 8554, 17, 7402, 2455, 1927, 5104, 2240, 22816, 1036, 1966, 3131, 1927, 43, 5738, 16896, 7032, 3145, 5572, 5289, 6377, 1958, 6202, 3316, 61, 18, 8849, 2909, 18, 3], "antigen": ["SAHHHHHHGSNTNIENIGDGAEVIKRTEDVSSKKWGVTQNVQFDFVKDKKYNKDALIVKMQGFINSRTSFSDVKGSGYELTKRMIWPFQYNIGLTTKDPNVSLINYLPKNKIETTDVGQTLGYNIGGNFQSAPSIGGNGSFNYSKTISYTQKSYVSEVDKQNSKSVKWGVKANEFVTPDGKKSAHDRYLFVQSPNGPTGSAREYFAPDNQLPPLVQSGFNPSFITTLSHEKGSSDTSEFELSYGRNLDITYATLFPRTGIYAERKHNAFVNRNFVVRYKVNWKTHEIKVKGHN"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A human Fab (IGHV1/IGKV3-Kappa) targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding. The antibody is designed as a neutralizing antibody capable of blocking ACE2 receptor engagement and suppressing spike-mediated membrane fusion, with maintained potency against the Delta variant (B.1.617 lineage).", "target_protein": "VQLQQSGPELVKPGASVKISCKASMNWMKQSPEKSLEWIGETDNQKFKAKATLTVDKSSSTAYMQLKSLTSEDSAVYYCWGQGTSVTVSKAGYSFTGYSINPSTGGTARSRGDY", "metadata": {"pdb_id": "7mw6", "light_chain_seq": "IVLTQSPASLAVSLGQRATISCRASESVEYYGTSLMQWYQQKPGQPPKVLIYAASNVESGVPARFSGSGSGTDFSLNIHPVEEDDIAMYFCQQSRKVPWTFGGGTKLEIKRT", "cdrh1_seq": "GYSFTGYS", "cdrh2_seq": "INPSTGGT", "cdrh3_seq": "ARSRGDY", "cdrl1_seq": "ESVEYYGTSL", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSRKVPWT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 101]", "cdrl1_pos": "[25, 34]", "cdrl2_pos": "[52, 54]", "cdrl3_pos": "[91, 99]", "cdrh3_split": "val", "cdrh3_cluster": "7mw5", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "potently neutralized SARS-CoV-2 WA1 and B.1.617 pseudoviruses"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 7131, 1927, 7472, 8298, 1028, 3148, 9577, 1930, 13556, 10429, 17, 3434, 3260, 5289, 16, 1956, 5514, 10397, 3316, 1920, 9649, 6031, 12, 44, 18, 21, 18, 5473, 1027, 7924, 13, 18, 3], "antigen": ["CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPEL"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human Fab (IGHV1/IGKV1-Kappa) targeting the engineered ectodomain of Receptor tyrosine-protein kinase erbB-3 (HER3). HER3 is a tyrosine-protein kinase that binds neuregulin-1 and is activated by it, promoting phosphatidylinositol 3-kinase association and myeloid cell differentiation regulation. This antibody is part of a bispecific IgG1 designed to inhibit HER3 signaling and downstream PI3K/Akt pathway activation in HER2-driven cancers resistant to HER2-targeting agents. Generate the corresponding HCDRs.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASMHWVRQAPGQGLEWMGWNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCWGQGTLVTVSSAGYTFTGYYINPNSGGTARDHGSRHFWSYWGFDY", "metadata": {"pdb_id": "5o4o", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPTFGQGTKVEIKRT", "cdrh1_seq": "GYTFTGYY", "cdrh2_seq": "INPNSGGT", "cdrh3_seq": "ARDHGSRHFWSYWGFDY", "cdrl1_seq": "QSISSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSYSTPPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5o4o", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Receptor tyrosine-protein kinase erbB-3, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "potently inhibits the HRG/HER3 pathway and downstream PI3K/Akt signaling"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11091, 27385, 1927, 3148, 6941, 17, 2213, 4016, 11954, 17, 23, 12, 3656, 1010, 13, 18, 3656, 1010, 1977, 43, 6941, 17, 2213, 4016, 1988, 6876, 2974, 6541, 3392, 17, 21, 1930, 1977, 4128, 2007, 2176, 16, 7356, 16927, 23, 17, 4016, 3279, 1930, 9677, 2024, 4155, 3640, 18, 2052, 3533, 1977, 3131, 1927, 43, 7266, 10231, 15368, 4609, 1942, 2875, 3656, 1010, 3197, 1930, 5863, 7734, 19, 5496, 3374, 2936, 1922, 9162, 17, 6446, 5717, 4910, 1942, 9162, 17, 5133, 4820, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["QPLVYNKLTFQLEPNPHTVRACPPDKMEVDKNGLKMCEPCGGLCPKACEGTGSGSRFQTVDSSNIDGFVNCTKILGNLDFLITGLNGDPWHKIPALDPEKLNVFRTVREITGYLNIQSWPPHMHNFSVFSNLTTIGGRSLYNRGFSLLIMKNLNVTSLGFRSLKEISAGRIYISANRQLCYHHSLNWTKVLRGPTEERLDIKHNRPRRDCVAEGKVCDPLCSSGGCWGPGPGQCLSCRNYSRGGVCVTHCNFLNGEPREFAHEAECFSCHPECQPMEGTATCNGSGSDTCAQCAHFRDGPHCVSSCPHGVLGAKGPIYKYPDVQNECRPCHENCTQGCKGPELQDCL"]} {"modality_type": "antibody", "text": "A murine Fab (IGHV3/IGKV14-Kappa) targeting Der f 1 variant, a cysteine protease allergen from the house dust mite Dermatophagoides farinae. Der f 1 is a thiol protease that hydrolyzes proteins with a preference for Phe or basic residues and elicits IgE responses in allergic subjects. The antibody is designed to recognize a cross-reactive epitope on Der f 1 that is associated with IgE recognition and can serve as a molecular target for allergen vaccine development. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "EVQLQESGPGLVKPSQSLSLTCTVTWNWIRQFPGNKLEWMGYSYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCWGQGTLVTVSAAGYSITSDYAISYSGTTGRTGVYRYPERAPY", "metadata": {"pdb_id": "5vpl", "light_chain_seq": "QIVMTQSPFSMYATLGERVTITCKASQDIYSYLSWLQQKPGKSLKTLIYRANRLITGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPYTFGGGTKLEMKRA", "cdrh1_seq": "GYSITSDYA", "cdrh2_seq": "ISYSGTT", "cdrh3_seq": "GRTGVYRYPERAPY", "cdrl1_seq": "QDIYSY", "cdrl2_seq": "RAN", "cdrl3_seq": "LQYDEFPYT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5vpl", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV14", "is_engineered": false, "target_antigen": "Der f 1 variant (Peptidase 1), Dermatophagoides farinae", "target_domain": null, "functional_role": "other", "evidence_quote": "binds to a unique cross-reactive epitope on both allergens associated with IgE recognition"}}}, "tokenized_instruction": [2, 43, 7135, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 1006, 17, 12093, 13, 5133, 3135, 48, 21, 6031, 16, 43, 8666, 7154, 15468, 2037, 1920, 5953, 14677, 24688, 13467, 4965, 12363, 5108, 24379, 18, 3135, 48, 21, 1977, 43, 13914, 7154, 1988, 7222, 20887, 2697, 1956, 43, 8308, 1958, 10422, 2014, 5937, 4248, 1930, 21809, 10777, 3387, 1922, 10519, 3297, 18, 1920, 3533, 1977, 4609, 1942, 9967, 43, 3567, 17, 6079, 10095, 1990, 3135, 48, 21, 1988, 1977, 2458, 1956, 10777, 5708, 1930, 2112, 7120, 1966, 43, 3272, 2758, 1958, 15468, 5955, 2740, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["TSACRINSVNVPSELDLRSLRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNTSLDLSEQELVDCASQHGCHGDTIPRGIEYIQQNGVVEERSYPYVAREQQCRRPNSQHYGISNYCQIYPPDVKQIREALTQTHTAIAVIIGIKDLRAFQHYDGRTIIQHDNGYQPNYHAVNIVGYGSTQGVDYWIVRNSWDTTWGDSGYGYFQAGNNLMMIEQYPYVVIM"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human Fab (IGHV3/IGLV3-Lambda) targeting the Large envelope protein of Hepatitis B virus genotype D. The Large envelope protein attaches the virus to cell receptors to initiate infection and mediates fusion between virion and endosomal membranes. This antibody is designed as a neutralizing antibody targeting the antigenic loop (AGL) region, which exhibits structural polymorphism across distinct HBsAg types and is recognized by different groups of neutralizing antibodies. Can you generate its HCDRs?", "target_protein": "ELQLVESGGGWVQPGGSQRLSCAASMSWVRQAPGKGLEWVATLYVDSVKGRFTISRDNAKNSLFLQMNNLRVEDTAVYYCWGQGTTVSVSSGRIFRSFYINQDGSEKAAWSGNSGGMDV", "metadata": {"pdb_id": "9jt1", "light_chain_seq": "YELTQPPSVSVSPGQTVSIPCSGDKLGNKNVCWFQHKPGQSPVLVIYEVKYRPSGIPERFSGSNSGNTATLTISGTQAMDEAAYFCQTWDSTTVVFGGGTRLTVL", "cdrh1_seq": "GRIFRSFY", "cdrh2_seq": "INQDGSEK", "cdrh3_seq": "AAWSGNSGGMDV", "cdrl1_seq": "KLGNKN", "cdrl2_seq": "EVK", "cdrl3_seq": "QTWDSTTVV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "9u9b", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "Large envelope protein, Hepatitis B virus genotype D", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibodies (NAbs) recognize HBsAg; NAbs in different groups may recognize distinct epitopes"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 28961, 1020, 1010, 17, 18279, 13, 5133, 1920, 3103, 11262, 2213, 1927, 7977, 44, 3413, 5619, 46, 18, 1920, 3103, 11262, 2213, 5823, 1918, 1920, 3413, 1942, 2024, 4086, 1942, 11051, 2909, 1930, 10412, 5289, 2192, 19230, 1930, 16514, 5726, 18, 2052, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 14606, 5881, 12, 2260, 1024, 13, 3031, 16, 2154, 9826, 4346, 8218, 3436, 4493, 17596, 3584, 1930, 1977, 6783, 2007, 2413, 2671, 1927, 12130, 3788, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["LLCLIFLLVLLDYQGMLPVCPLITSTGPCRTCMTTAQGTSMYPSCCCTKPSDGNCTCIPIPSSWAFGKFLWEWASA"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human Fab, DH1047 (IGHV1/IGKV4-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors, initiating infection and triggering conformational changes that lead to fusion of viral and cellular membranes. The antibody is designed as a neutralizing antibody targeting the RBD outer face, binding within the Receptor-binding domain (RBD). Can you generate its HCDRs?", "target_protein": "QVQLVQSGAEVKKPGASVQVSCQASIHWVRQAPGQGLEWMGIIYAQGFQGRVTMTRDTSLNTIYLELSSLRSEDTAVYYCWGQGTLVTVSSAANTFTNHYIYPTGGNTARDVRVDDSWSGYDLLSGGTYFDY", "metadata": {"pdb_id": "8dtk", "light_chain_seq": "DIVMTQSPDSLAVSLGERATINCRSSQSVLYSSNNENYLAWYQQKPGQPPKLLIYWASTRESGIPDRFSGSGSGTDFTLTISRLQAEDVAVYYCQQYYSLPRTFGQGTKVEIK", "cdrh1_seq": "ANTFTNHY", "cdrh2_seq": "IYPTGGNT", "cdrh3_seq": "ARDVRVDDSWSGYDLLSGGTYFDY", "cdrl1_seq": "QSVLYSSNNENY", "cdrl2_seq": "WAS", "cdrl3_seq": "QQYYSLPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 119]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 102]", "cdrh3_split": "val", "cdrh3_cluster": "8dtk", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DH1047", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "RBD directed antibody DH1047"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 6914, 16, 6781, 15231, 1027, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 16, 12410, 2909, 1930, 14074, 8523, 2840, 1988, 2949, 1942, 5289, 1927, 4324, 1930, 3689, 5726, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 25780, 7642, 6171, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["PNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTN"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A human Fab, P5A-2G9 (IGHV3/IGLV5-Lambda), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that competes with ACE2 for RBD binding, targeting the receptor-binding domain (RBD) with substantial overlap to the ACE2-binding site.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVAVYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTFSSYGIWYDGSNKARWFHTGGYFDY", "metadata": {"pdb_id": "7czt", "light_chain_seq": "QPVLTQPPSSSASPGESARLTCTLPSDINVSSYNIYWYQQKPGSPPRYLLYYYSDSDKGQGSGVPSRFSGSKDASANTGILLISGLQSEDEADYYCMIWPSNALYVFGTGTKVTVLGQ", "cdrh1_seq": "GFTFSSYG", "cdrh2_seq": "IWYDGSNK", "cdrh3_seq": "ARWFHTGGYFDY", "cdrl1_seq": "SDINVSSYN", "cdrl2_seq": "YYSDSDK", "cdrl3_seq": "MIWPSNALYV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[25, 33]", "cdrl2_pos": "[51, 57]", "cdrl3_pos": "[96, 105]", "cdrh3_split": "val", "cdrh3_cluster": "7czt", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "P5A-2G9", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV5", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibodies capable of disrupting proper interaction between the receptor binding domain (RBD) and ACE2"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 2616, 6914, 16, 18974, 1019, 17, 16424, 1026, 12, 20733, 1020, 1010, 19, 28961, 1020, 1015, 17, 18279, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 17269, 1036, 1956, 8298, 1028, 1958, 25780, 2743, 16, 5133, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 1956, 6317, 7713, 1942, 1920, 8298, 1028, 17, 2743, 3200, 18, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVMESEFRVYSSANNCTFEYVSKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A human Fab, MEDI7814 (IGHV3/IGLV2-Lambda), targeting Complement C5 of Homo sapiens. Complement C5 is a precursor of the C5a anaphylatoxin and C5b component of the complement cascade, which leads to phagocytosis and breakdown of pathogens, and is a component of the membrane attack complex that inserts into target cell membranes to cause cell lysis. The antibody is designed as a neutralizing antibody that blocks C5a and C5adesArg binding to both C5aR1 and C5aR2 receptors while preserving complement-mediated bacterial cell killing. Please provide the HCDR sequences.", "target_protein": "EVQLLESGGGLVQPGGSLRLSCAASMSWVRQAPGKGLEWVSAYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTMVTVSGFTFSSYAISGSGGSTARDDDYEEWPWYYGMDV", "metadata": {"pdb_id": "4uu9", "light_chain_seq": "QSALTQPASVSGSPGQSITISCTGTSSDIGGSKYVSWYQQHPGKAPKLIIFDVNRRPSGLSNRFSASKSGNTASLTISGLQAEDEADYYCTSYHPTKTILFGGGTKLTVL", "cdrh1_seq": "GFTFSSYA", "cdrh2_seq": "ISGSGGST", "cdrh3_seq": "ARDDDYEEWPWYYGMDV", "cdrl1_seq": "SSDIGGSKY", "cdrl2_seq": "DVN", "cdrl3_seq": "TSYHPTKTIL", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[25, 33]", "cdrl2_pos": "[51, 53]", "cdrl3_pos": "[90, 99]", "cdrh3_split": "val", "cdrh3_cluster": "4uu9", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "MEDI7814", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Complement C5, Homo sapiens", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizes C5a and C5adesArg binding to the C5aR1 and C5aR2 receptors"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 2616, 6914, 16, 2701, 7950, 3745, 12, 20733, 1020, 1010, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 5508, 13441, 1927, 16350, 27974, 18, 5508, 13441, 1977, 43, 7897, 1927, 1920, 28266, 21219, 22956, 1930, 13441, 1014, 4594, 1927, 1920, 5508, 9861, 16, 2154, 5029, 1942, 13715, 1930, 13630, 1927, 7741, 16, 1930, 1977, 43, 4594, 1927, 1920, 3260, 8926, 2796, 1988, 17520, 2460, 2758, 2024, 5726, 1942, 3936, 2024, 8502, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 28266, 1930, 28266, 7980, 2419, 2743, 1942, 2321, 28266, 7011, 1930, 28266, 9746, 4086, 2679, 17701, 5508, 17, 3434, 4543, 2024, 11879, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["STLQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISLGPRCIKAFTECCVVASQLRANI"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, 6516 (IGHV1/IGKV1-Kappa), targeting the Spike glycoprotein of Human betacoronavirus 2c EMC/2012 (MERS-CoV). The Spike glycoprotein attaches the virion to the cell membrane by interacting with the host receptor to initiate infection and acts as a viral fusion peptide following S2 cleavage. The antibody is designed as a neutralizing antibody against MERS-CoV.", "target_protein": "EVQLVQSGAEVKKPGSSVKVSCKASICWVRQAPGQGLEWMGGNYAQKFQGRVTITADESTSTVYMELSSLRSEDTAVYYCWGQGTTVTVSSAGGTFSSYAIIPFFGTVANSYCSSTNCYRYYQNGLDV", "metadata": {"pdb_id": "7v3l", "light_chain_seq": "AIRMTQSPVTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASTLQSGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYDNYSQLTFGPGTKLEIKRT", "cdrh1_seq": "GGTFSSYA", "cdrh2_seq": "IIPFFGTV", "cdrh3_seq": "ANSYCSSTNCYRYYQNGLDV", "cdrl1_seq": "QSISSW", "cdrl2_seq": "KAS", "cdrl3_seq": "QQYDNYSQLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "7v3l", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "6516", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Spike glycoprotein, Human betacoronavirus 2c EMC/2012", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 4459, 3672, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 2616, 4666, 4879, 2830, 10703, 6921, 2391, 1030, 19, 3775, 12, 20197, 17, 6083, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 1920, 4423, 3148, 1942, 11051, 2909, 1930, 8016, 1966, 43, 4324, 5289, 4207, 2894, 5159, 6404, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 3316, 20197, 17, 6083, 18, 3], "antigen": ["YVDVGPDSVKSACIEVDIQQTFFDKTWPRPIDVSKADGIIYPQGRTYSNITITYQGLFPYQGDHGDMYVSAGHATGTTPQKLFVANYSQDVKQFANGFVVRIGAAANSTGTVIISPSTSATIRKIYPAFMLGSSVGNFSDGKMGRFFNHTLVLLPDGCGTLLRAFYCILEPRSGNHCPAGNSYTSFATYHTPATDCSDGNYNRNASLNSFKEYFNLRNCTFMYTYNITEDEILEWFGITQTAQGVHLFSSRYVDLYGGNMFQFATLPVYDTIKYYSIIPHSIRSIQSDRKAWAAFYVYKLQPLTFLLDFSVDGYIRRAIDCGFNDLSQLHCSYESFDVESGVYSVSSFEAKPSGSVVEQECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPIASQLGNCVEYSLYGVSGRGVFQNCTAVGVRQQRFVYDAYQNLVGYYSDDGNYYCLRACVSVPVSVIYDKETKTHATLFGSVACEHISSTMSQYSSTRSMLKPVGCVLGLVNSSLFVEDCKLPLGQSLCALPDTPSMRLASIAFNHPIQVDQLNSSYFKLSIPTNFSFGVTQEYIQTTIQKVTVDCKQYVCNGFQKCEQLLREYGQFCSKINQALHGANLRQDDSVRNLFASVKSSQSSPIIPGFGGDFNLTLLEPVARSAIEDLLFDKVTIADPGYMQGYDDCMQQICAQYVAGYKVLPPLMDVNMEAAYTSSLLGSIAGVGWTAGLSSFAAIPFAQSIFYRLNGVGITQQVLSENQKLIANKFNQALGAMQTGFTTTNEAFQKVQDAVNNNAQALSKLASELSNTFGAISASIGDIIQRLDVLEQDAQIDRLINGRLTTLNAFVAQQLVRSESAALSAQLAKDKVNECVKAQSKRSGFCGQGTHIVSFVVNAPNGLYFMHVGYYPSNHIEVVSAYGLCDAANPTNCIAPNGYFITNNTIVDEWSYTGSSFYAPEPITSLNTKYVA"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A human Fab, S1V2-83 (IGHV3/IGKV1-Kappa), targeting the engineered Hemagglutinin of Influenza A virus (A/Moscow/10/1999(H3N2)). Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and is responsible for fusion of the viral and endosomal membranes. The antibody is designed to target the conserved head interface epitope and confer protection against influenza infection via Fc-mediated effector mechanisms, with breadth across multiple HA serotypes.", "target_protein": "QVQLVESGGGVVQPGRSVRLTCAGSMNWVRQAPGKGLEWLAIWYADSVKGRFTISRDDAKNTLFLQMNSLTAEDTAVYYCWGQGTTVTVSGAGFSFSNFGISYDGSKKSKDRGDVWSGYYRGGDYHYYFGMDV", "metadata": {"pdb_id": "6xpz", "light_chain_seq": "DIQMTQSPSSLSTSVGDRVTITCQASQDISNFLNWYQQKPGKAPELLIYDASYLQGGVPSRFSGSGSGTDFSFTISSLQPEDIATYYCQQYNSLPITFGQGTRLEIKRT", "cdrh1_seq": "GFSFSNFG", "cdrh2_seq": "ISYDGSKK", "cdrh3_seq": "SKDRGDVWSGYYRGGDYHYYFGMDV", "cdrl1_seq": "QDISNF", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYNSLPIT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 120]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6xpz", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S1V2-83", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus (A/Moscow/10/1999(H3N2))", "target_domain": null, "functional_role": "other", "evidence_quote": "nonneutralizing antibodies protect mice from lethal challenge by Fc-mediated mechanisms"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 4062, 15755, 17, 5893, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 26141, 1927, 7108, 43, 3413, 12, 43, 19, 7500, 4879, 1018, 19, 2119, 19, 5372, 12, 25234, 13, 13, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 1977, 5061, 1958, 5289, 1927, 1920, 4324, 1930, 16514, 5726, 18, 1920, 3533, 1977, 4609, 1942, 2758, 1920, 5305, 4469, 6854, 10095, 1930, 7909, 6202, 3316, 7108, 2909, 3454, 6437, 17, 3434, 7917, 3531, 16, 1956, 22532, 3436, 3137, 2118, 16967, 18, 3], "antigen": ["ELVQSSSTGRICDSPHQILDGENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVAQNGTSSACKRRSIKSFFSRLNWLHQLENRYPALNVTMPNNDKFDKLYIWGVHHPSTDSVQTSVYVQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRY"]} {"modality_type": "antibody", "text": "What would be the HCDR sequences of an antibody with the following function: A murine Fab, vFP16.02 (IGHV1/IGKV1-Kappa), targeting the N-terminal fusion peptide of HIV-1 Envelope glycoprotein gp160. The fusion peptide is a critical component of the viral entry machinery that mediates fusion of viral and host cell membranes. The antibody is designed as a vaccine-elicited neutralizing antibody targeting the exposed N-terminal residues of the fusion peptide to achieve cross-clade neutralization breadth, binding within the Fusion peptide.", "target_protein": "QVQLLQSGAELVRPGASVTLSCKASIHWVKQTPVRGLDWIGAASNQKVKGRAILTADKSSSTAYMELRSLTSEDSAVYYCWGTGTTVTVSSAGYAFSDYEFDPKSGASTRLRYFGYFDV", "metadata": {"pdb_id": "6cdo", "light_chain_seq": "DVLMTQTPLSLPVSLGGQASISCRSSQSVVYSDGDTYLEWYLQKPGQSPKLLIYKVSRRFSGVPDRFSGSGSGTDFTLKISRVETEDLGVYYCFQGSHVPYTFGGGTKLEIKRT", "cdrh1_seq": "GYAFSDYE", "cdrh2_seq": "FDPKSGAS", "cdrh3_seq": "TRLRYFGYFDV", "cdrl1_seq": "QSVVYSDGDTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQGSHVPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "6wx2", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "vFP16.02", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "HIV-1 fusion peptide (residues 512-519), Human immunodeficiency virus 1", "target_domain": "Fusion peptide", "functional_role": "neutralizing", "evidence_quote": "vaccine-elicited FP-directed antibodies with promising neutralization breadth"}}}, "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 15691, 5113, 1016, 18, 5725, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 56, 17, 4262, 5289, 4207, 1927, 3525, 17, 21, 11262, 11424, 4882, 16954, 18, 1920, 5289, 4207, 1977, 43, 4140, 4594, 1927, 1920, 4324, 6904, 10853, 1988, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 18, 1920, 3533, 1977, 4609, 1966, 43, 5955, 17, 9856, 12130, 3533, 5133, 1920, 4616, 56, 17, 4262, 4248, 1927, 1920, 5289, 4207, 1942, 6230, 3567, 17, 11315, 14377, 22532, 16, 2743, 2651, 1920, 5289, 4207, 18, 3], "antigen": ["AVGIGAVF"]} {"modality_type": "antibody", "text": "What would be the HCDR sequences of an antibody with the following function: A murine Fab, 3F1 (IGHV1/IGKV6-Kappa), targeting a bis-STn glycopeptide derived from Mucin-1 subunit beta. Mucin-1 is a human protein with roles in cell adhesion, protection of epithelial cells, and cell signaling through phosphorylation and protein-protein interactions. This antibody forms a complex with the Mucin-1 glycopeptide antigen.", "target_protein": "QVQLKQSDAELVKPGASVKISCKASIHWVKQKPEQGLDWIGYKYNEKFKDKVTLTADKSSSTASMHLNSLTSEDSAVYFCWGQGTTLTVSSAGYTFTDHAISPGNGDIKRSLLALDY", "metadata": {"pdb_id": "8s6t", "light_chain_seq": "DILMTQSHKFMSTSVGDRVSITCKASQDVGTNIAWYQQKPGRSPKVLIYSASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLTDYFCQQYSSFPLTFGVGTKLELKRA", "cdrh1_seq": "GYTFTDHA", "cdrh2_seq": "ISPGNGDI", "cdrh3_seq": "KRSLLALDY", "cdrl1_seq": "QDVGTN", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYSSFPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 104]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8s6t", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": false, "target_antigen": "Mucin-1 subunit beta, synthetic construct", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 15090, 1009, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 43, 7266, 17, 21667, 8821, 8253, 3595, 2037, 14455, 17, 21, 5903, 4666, 18, 14455, 17, 21, 1977, 43, 2616, 2213, 1956, 5456, 1922, 2024, 6141, 16, 6202, 1927, 4944, 2094, 16, 1930, 2024, 3197, 2596, 4050, 1930, 2213, 17, 2213, 3719, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 14455, 17, 21, 8821, 8253, 4730, 18, 3], "antigen": ["ST"]} {"modality_type": "antibody", "text": "I want an antibody that has the function: A human Fab, DH1047 (IGHV1/IGKV4-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. DH1047 is designed as a broadly neutralizing antibody with cross-reactivity to SARS-CoV and bat coronavirus spike proteins, binding to RBD-up conformations. Output the HCDRs.", "target_protein": "QVQLVQSGAEVKKPGASVQVSCQASIHWVRQAPGQGLEWMGIIYAQGFQGRVTMTRDTSLNTIYLELSSLRSEDTAVYYCWGQGTLVTVSSAANTFTNHYIYPTGGNTARDVRVDDSWSGYDLLSGGTYFDY", "metadata": {"pdb_id": "7ld1", "light_chain_seq": "DIVMTQSPDSLAVSLGERATINCRSSQSVLYSSNNENYLAWYQQKPGQPPKLLIYWASTRESGIPDRFSGSGSGTDFTLTISRLQAEDVAVYYCQQYYSLPRTFGQGTKVEIKRT", "cdrh1_seq": "ANTFTNHY", "cdrh2_seq": "IYPTGGNT", "cdrh3_seq": "ARDVRVDDSWSGYDLLSGGTYFDY", "cdrl1_seq": "QSVLYSSNNENY", "cdrl2_seq": "WAS", "cdrl3_seq": "QQYYSLPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 119]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 102]", "cdrh3_split": "val", "cdrh3_cluster": "8dtk", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DH1047", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "DH1047 cross-reacted with SARS-CoV and SARS-CoV-2 S and protected mice from SARS-related bat coronavirus infection"}}}, "tokenized_instruction": [2, 51, 12914, 1925, 3533, 1988, 2258, 1920, 2347, 30, 43, 2616, 6914, 16, 6781, 15231, 1027, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 6781, 15231, 1027, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1956, 3567, 17, 8229, 1942, 20466, 17, 6083, 1930, 11579, 5548, 10703, 10429, 2697, 16, 2743, 1942, 25780, 17, 2353, 12526, 18, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFNNCTFEYVSFKNLREFVFKNYFKIYSKHTPINDLPQGFSALEPLVDLPIGINITRFQTLLAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRKPFERPLQSYGFQPTNGVGYQPYRVVVLSFATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNEVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKSKRSFIEDLLFNKVTKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab (IGHV1/IGKV3-Kappa) targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2, specifically the B.1.617.1 (kappa) variant. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors (ACE2, NRP1/NRP2, ASGR1, or integrin) to initiate infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. This antibody forms a complex with the Spike glycoprotein. Please output the HCDRs.", "target_protein": "VQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7sob", "light_chain_seq": "VLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 114]", "cdrl1_pos": "[24, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 94]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 16, 4475, 1920, 44, 18, 21, 18, 5473, 1027, 18, 21, 12, 12093, 13, 6031, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 12, 8298, 1028, 16, 5214, 5113, 19, 5214, 5991, 16, 1966, 2299, 1009, 16, 2014, 8920, 13, 1942, 11051, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 11424, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["QCVNLQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHADNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYMKSEFRVYSSANNCTFEYVSQPFLMFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVCPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSTPCNGVQGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLCPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAHEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPEL"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A murine Fab (IGHV7/IGKV10-Kappa) targeting the Minor capsid protein A1 of Escherichia phage Qbeta. The Minor capsid protein A1 self-assembles to form an icosahedral capsid with T=3 symmetry and is involved in viral genome encapsidation and translational repression of viral replicase synthesis. This antibody forms a complex with the Minor capsid protein A1 dimer.", "target_protein": "EVQLQESGGGLVQPGGSLSLSCAASMSWVRQPPGKALEWLGFEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCWGQVTTLGFTFTDYYIRIKANSYTTARSPDYYGGYYFDY", "metadata": {"pdb_id": "8w5h", "light_chain_seq": "IQMTQTTSSLSASLGDRVTITCRASQVISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPYTFGGGTKL", "cdrh1_seq": "GFTFTDYY", "cdrh2_seq": "IRIKANSYTT", "cdrh3_seq": "ARSPDYYGGYYFDY", "cdrl1_seq": "QVISNY", "cdrl2_seq": "YTS", "cdrl3_seq": "QQGNTLPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 111]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "8w5h", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV7", "light_subclass": "IGKV10", "is_engineered": false, "target_antigen": "Minor capsid protein A1, Escherichia phage Qbeta", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 1020, 1027, 19, 7021, 1040, 7390, 1008, 17, 12093, 13, 5133, 1920, 5857, 14681, 2213, 8080, 1927, 10210, 10503, 59, 20440, 18, 1920, 5857, 14681, 2213, 8080, 3543, 17, 17421, 1036, 1942, 2386, 1925, 29310, 24704, 14681, 1956, 62, 33, 23, 12572, 1930, 1977, 3286, 1922, 4324, 3843, 10771, 20356, 1930, 8414, 10084, 1927, 4324, 5825, 2051, 4271, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 5857, 14681, 2213, 8080, 7632, 18, 3], "antigen": ["AKLETVTLGNIGKDGKQTLVLNPRGVNPTNGVASLSQAGAVPALEKRVTVSVSQPSRNRKNYKVQVKIQNPTACTANGSCDPSVTRQAYADVTFSFTQYSTDEERAFVRTELAALLASPLLIDAIDQLNPAY"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (BA.2.75 variant). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes through class I viral fusion protein mechanisms. The antibody is designed as a neutralizing antibody targeting a conserved epitope recognized across sarbecoviruses, maintaining activity against the BA.2.75 variant despite immune evasion by other neutralizing antibodies.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7yqx", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKR", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "S309 recovered its binding activity against BA.2.75 RBD and exhibited slightly improved neutralization activity against BA.2.75"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 6813, 18, 22, 18, 4089, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 2921, 51, 4324, 5289, 2213, 3531, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 43, 5305, 10095, 6783, 3436, 9851, 12409, 18368, 16, 8231, 2455, 3316, 1920, 6813, 18, 22, 18, 4089, 6031, 4281, 3743, 25092, 2007, 2303, 12130, 3788, 18, 3], "antigen": ["TQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHENNKSRMESELRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPVNLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSSWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFHEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPE"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A human Fab, MEDI-579 (IGHV1/IGKV1-Kappa), targeting Plasminogen activator inhibitor 1 (PAI-1), a serine protease inhibitor that regulates fibrinolysis, cell adhesion and cell motility through interactions with plasminogen activators and vitronectin. The antibody is designed to selectively inhibit the interaction of PAI-1 with tissue-type and urokinase-type plasminogen activators while preserving PAI-1 binding to vitronectin, thereby modulating PAI-1's protease-inhibitory function in disease settings such as lupus nephritis and diabetic kidney disease. Please generate its HCDRs.", "target_protein": "QVQLVQSGAEVKKPGSSVKVSCKASISWVRQAPGQGLEWMGGNYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCWGRGTLVTVSSAGGTFSSYAIIPTFGTAARERRQWLEGHFDY", "metadata": {"pdb_id": "6i8s", "light_chain_seq": "DIQMTQSPSTLSASVGDRVTITCRASEGIYHNLAWYQQKPGKAPKLLIYKASSLASGVPSRFSGSRSGTEFTLTISSLQPDDFATYYCQQYSNYPLTFGGGTKVEIKRT", "cdrh1_seq": "GGTFSSYA", "cdrh2_seq": "IIPTFGTA", "cdrh3_seq": "ARERRQWLEGHFDY", "cdrl1_seq": "EGIYHN", "cdrl2_seq": "KAS", "cdrl3_seq": "QQYSNYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6i8s", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "MEDI-579", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Plasminogen activator inhibitor 1, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "specifically inhibits serine protease interactions with PAI-1 while conserving vitronectin binding"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 2701, 17, 4786, 1026, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 17485, 9518, 4106, 21, 12, 15885, 17, 21, 13, 16, 43, 8468, 7154, 4106, 1988, 7014, 9450, 6892, 16, 2024, 6141, 1930, 2024, 9254, 2596, 3719, 1956, 17485, 15497, 1930, 3596, 2912, 2341, 1921, 18, 1920, 3533, 1977, 4609, 1942, 9331, 2875, 1920, 2835, 1927, 15885, 17, 21, 1956, 2960, 17, 2601, 1930, 14984, 25545, 17, 2601, 17485, 15497, 2679, 17701, 15885, 17, 21, 2743, 1942, 3596, 2912, 2341, 1921, 16, 6113, 10871, 15885, 17, 21, 11, 61, 7154, 17, 5431, 2347, 1922, 2573, 6457, 2427, 1966, 13711, 25064, 1930, 6152, 5245, 2573, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["SYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRSTVKQVDFSEVERARFIINDWVKTHTKGMISHLLGTGAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAPYEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRQFQADFTSLSDQEPLHVALALQKVKIEVNESGTARMAPEEIIIDRPFLFVVRHNPTGTVLFMGQVMEP"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A murine Fab (IGHV3/IGKV1-Kappa) targeting the pH-gated potassium channel KcsA of Streptomyces lividans. KcsA acts as a pH-gated potassium ion channel; changing the cytosolic pH from 7 to 4 opens the channel, with monovalent cation preference K(+) > Rb(+) > NH4(+) >> Na(+) > Li(+). This antibody is designed as a crystallographic chaperone to stabilize the full-length channel in its closed conformation for structural determination.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVASYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFNISSYSISSYYSSTARQPSYHMYSWWVALDY", "metadata": {"pdb_id": "3eff", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASFLESGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYYSYSAPVTFGQGTKVEIKRT", "cdrh1_seq": "GFNISSYS", "cdrh2_seq": "ISSYYSST", "cdrh3_seq": "ARQPSYHMYSWWVALDY", "cdrl1_seq": "QSVSSA", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYYSYSAPVT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "3pjs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "pH-gated potassium channel KcsA, Streptomyces lividans", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "synthetic antigen-binding fragments (Fabs) as crystallographic chaperones"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 2087, 17, 12336, 9057, 4999, 29971, 1019, 1927, 22874, 15260, 9532, 3355, 18, 29971, 1019, 8016, 1966, 43, 2087, 17, 12336, 9057, 4755, 4999, 31, 8546, 1920, 9410, 2087, 2037, 27, 1942, 24, 19851, 1920, 4999, 16, 1956, 28685, 9976, 8308, 53, 12, 15, 13, 34, 6160, 12, 15, 13, 34, 14945, 12, 15, 13, 34, 34, 4049, 12, 15, 13, 34, 2336, 12, 15, 13, 18, 2052, 3533, 1977, 4609, 1966, 43, 17832, 14044, 1942, 13448, 1920, 4125, 17, 3471, 4999, 1922, 2496, 8047, 7748, 1958, 4346, 7063, 18, 3], "antigen": ["SALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRLVAVVVMVAGITSFGLVTAALATWFVGREQERRGHFVRHSEKAAEEAYTRTTRALHERFDRLERMLDDNRR"]} {"modality_type": "antibody", "text": "Here is the antibody function: A rhesus macaque Fab, K11 (IGHV4/IGKV1-Kappa), targeting the Envelope glycoprotein gp120 of Simian immunodeficiency virus. The surface protein gp120 attaches the virus to the host lymphoid cell by binding to the primary receptor CD4, inducing structural rearrangement that creates a high-affinity binding site for a chemokine coreceptor, and also targets the virus to gut-associated lymphoid tissue by binding host integrins. The antibody is designed as a neutralizing antibody targeting the glycan hole epitope on gp120, which is a conserved neutralizing epitope among SIVmac239-infected rhesus macaques. Generate the corresponding HCDRs.", "target_protein": "QLQESGPGVVRPSQTLSLTCAVSWTWIRQPPGKGLEWIGNNYNPSLKTRISISKDMSKNQFSLKLNSLTATDTAIYYCWGQGVLVTVSSGDTVSSCCFFISYDNDNTARESPSRGNFCYAYLYGNCPLHFDL", "metadata": {"pdb_id": "7t2p", "light_chain_seq": "DILLTQSPSSLSGSVGDRVTITCRASQGINSYLNWYQQKPGKAPKLLIYFANRLQSGVPSRFSGSGSGTEFTLTISSLQSEDGATYYCQQYDTFPTFGPGTKLDIK", "cdrh1_seq": "GDTVSSCCFF", "cdrh2_seq": "ISYDNDNT", "cdrh3_seq": "ARESPSRGNFCYAYLYGNCPLHFDL", "cdrl1_seq": "QGINSY", "cdrl2_seq": "FAN", "cdrl3_seq": "QQYDTFPT", "cdrh1_pos": "[23, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 120]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "7t2p", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "K11", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp120, Simian immunodeficiency virus", "target_domain": "glycan hole", "functional_role": "neutralizing", "evidence_quote": "K11 neutralized SIVmac239 at an IC50 of 0.12 \u03bcg/mL; K11 showed protection after two challenges"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 16996, 20533, 6914, 16, 16185, 1009, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 16102, 1927, 30130, 13141, 3413, 18, 1920, 3154, 2213, 16102, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1988, 15628, 43, 2149, 17, 5173, 2743, 3200, 1958, 43, 11673, 30435, 2684, 16, 1930, 2222, 4845, 1920, 3413, 1942, 7660, 17, 2458, 11751, 2960, 2007, 2743, 4423, 15563, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 15060, 13356, 10095, 1990, 16102, 16, 2154, 1977, 43, 5305, 12130, 10095, 2706, 14398, 26016, 24480, 17, 4014, 16996, 18161, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["TLYVTVFYGVPAWRNATIPLFCATKNRDTWGTTQCLPDNGDYSEMALNVTESFDAWNNTVTEQAIEDVWQLFETSIKPCVKLSPLCITMRCNKSETDRWGLTKSITTTASTTSTTASAKVDMVNETSSCIAQDNCTGLEQEQMISCKFNMTGLKRDKSKEYNETWYSADLVCEQGNNTGNESRCYMNHCNTSVIQESCDKHYWDAIRFRYCAPPGYALLRCNDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFNGTRAENRTYIYWHGRDNRTIISLNKYYNLTMKCRRPGNKTVLPVTIMSGLVFHSQPINDRPKQAWCWFGGKWKDAIKEVKQTIVKHPRYTGTNNTDKINLTAPGGGDPEVTFMWTNCRGEFLYCKMNWFLNWVEDRNTANQKPKEQHKRNYVPCHIRQIINTWHKVGKNVYLPPREGDLTCNSTVTSLIANIDWIDGNQTNITMSAEVAELYRLELGDYKLVEITPIGLAPTSCKRY", "GFLGFLATAGSAMGAASLTLTAQSRTLLAGIVQQQQQLLDVPKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWGCAFRQVCCTTVPWPNASLIPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKL"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (C.37 Lambda variant). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptor ACE2, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting the receptor-binding domain to prevent receptor engagement and viral entry.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "8vyg", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEI", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "RBD-targeting nAb"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 45, 18, 3191, 18279, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 3148, 8298, 1028, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 3148, 17, 2743, 3418, 1942, 4625, 3148, 9577, 1930, 4324, 6904, 18, 3], "antigen": ["NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVCPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYQYRLFRKSNLKPFERDISTEIVEGFNCYSPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab, D1 H1-17/H3-14 (IGHV4/IGKV1-Kappa), targeting the engineered Hemagglutinin head domain of Influenza A virus (A/Texas/50/2012(H3N2)). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for membrane fusion. The antibody is designed to target a conserved head interface epitope and confer protection against influenza infection via Fc-mediated effector mechanisms, with breadth across multiple HA serotypes. Please output the HCDRs.", "target_protein": "QVQLQESGPGLVKPSESLSLTCSVSWSWIRQLPGKGLEWIGYKYNPSLNGRVTLSIDASKNQFSLELSSVTAADTAVYYCWGQGTMVTVSGAGGSVSSNLHYISYTGSTARDFFEKLIADDLNAFDI", "metadata": {"pdb_id": "6xpq", "light_chain_seq": "DIRVTQSPSSLSASVGDRVTITCRASQSISRSLNWYQQRPGKAPKFLIYAASNLQSGVPSRFSGGGSGTDFTLTISSLQPEDFATYYCQETYSRTFGQGTKADIKRT", "cdrh1_seq": "GGSVSSNLHY", "cdrh2_seq": "ISYTGST", "cdrh3_seq": "ARDFFEKLIADDLNAFDI", "cdrl1_seq": "QSISRS", "cdrl2_seq": "AAS", "cdrl3_seq": "QETYSRT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 114]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 94]", "cdrh3_split": "val", "cdrh3_cluster": "6xpq", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "D1 H1-17/H3-14", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus (A/Texas/50/2012(H3N2))", "target_domain": null, "functional_role": "other", "evidence_quote": "members of both of these classes of nonneutralizing antibodies protect mice from lethal challenge by Fc-mediated mechanisms"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 8524, 9169, 17, 2752, 19, 8170, 17, 2607, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 26141, 4469, 3418, 1927, 7108, 43, 3413, 12, 43, 19, 14477, 19, 2761, 19, 3775, 12, 25234, 13, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1942, 2758, 43, 5305, 4469, 6854, 10095, 1930, 7909, 6202, 3316, 7108, 2909, 3454, 6437, 17, 3434, 7917, 3531, 16, 1956, 22532, 3436, 3137, 2118, 16967, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["ATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWNGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPVTDKDQIFLYAQPSGRITVSTKRSQQAVIPNIGFRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQS"]} {"modality_type": "antibody", "text": "What would be the HCDR sequences of an antibody with the following function: Chicken Fab antibodies targeting the Cysteine-rich protective antigen (CyRPA) of Plasmodium falciparum 3D7. CyRPA is essential for invasion of host erythrocytes by blood stage merozoites and is required for assembly of the PfRH5 adhesion complex, which facilitates binding to host receptor BSG/basigin and establishment of a tight junction between merozoite and erythrocyte membranes. The antibodies are designed to inhibit parasite growth and, when paired with non-competing antibodies targeting neighbouring epitopes, to achieve synergistic growth-inhibitory activity through heterotypic antibody interactions.", "target_protein": "VTLDESGGGLQTPGGALSLVCKASMGWVRQAPGKGLEYVAGLYTPAVKGRATISRDNGQSTVRLQLNNLRAEDTATYFCWGHGTEVIVSSAGFDFSSYAIRNDGSFTTKSADDGGHYSDFSGEIDA", "metadata": {"pdb_id": "7pi3", "light_chain_seq": "LTQPSSVSANPGETVKITCSGSTYNYGWYQQKSPGSAPVTVIYYNDKRPSDIPSRFSGSKSGSTGTLTITGVQAEDEAVYYCGNSDSRNVAFGAGTTLTVLRT", "cdrh1_seq": "GFDFSSYA", "cdrh2_seq": "IRNDGSFT", "cdrh3_seq": "TKSADDGGHYSDFSGEIDA", "cdrl1_seq": "TYNY", "cdrl2_seq": "YND", "cdrl3_seq": "GNSDSRNVA", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 113]", "cdrl1_pos": "[22, 25]", "cdrl2_pos": "[43, 45]", "cdrl3_pos": "[82, 90]", "cdrh3_split": "val", "cdrh3_cluster": "7phw", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": null, "light_subclass": null, "is_engineered": false, "target_antigen": "Cysteine-rich protective antigen, Plasmodium falciparum", "target_domain": null, "functional_role": "other", "evidence_quote": "strongly inhibit parasite growth in in vitro assays"}}}, "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 11218, 6914, 3788, 5133, 1920, 8666, 17, 5536, 6337, 4730, 12, 6002, 11119, 1019, 13, 1927, 15663, 13098, 5050, 1027, 18, 6002, 11119, 1019, 1977, 4415, 1958, 6254, 1927, 4423, 14161, 2007, 2877, 3587, 6902, 21831, 1930, 1977, 3414, 1958, 5957, 1927, 1920, 5099, 5004, 1015, 6141, 2796, 16, 2154, 11374, 2743, 1942, 4423, 3148, 8242, 1029, 19, 2726, 1950, 1921, 1930, 11108, 1927, 43, 8246, 6910, 2192, 6902, 26553, 1930, 15469, 5726, 18, 1920, 3788, 2032, 4609, 1942, 2875, 8652, 2905, 1930, 16, 2469, 7304, 1956, 2447, 17, 11743, 3788, 5133, 24318, 11427, 16, 1942, 6230, 11322, 2905, 17, 5431, 2455, 2596, 19732, 5518, 1935, 3533, 3719, 18, 3], "antigen": ["RHVFIRTELSFIKNNVPCIRDMFFIYKRELYNICLDDLKGEEDETHIYVQKKVKDSWITLNDLFKETDLTGRPHIFAYVDVEEIIILLCEDEEFSNRKKDMTCHRFYSNDGKEYNNAEITISDYILKDKLLSSYVSLPLKIENREYFLICGVSPYKFKDDDILCMASHDKGETWGTKIVIKYDNYKLGVQYFFLRPYISKNDLSFHFYVGDNINNVKNVNFIECTHEKDLEFVCSNRDFLKDNKVLQDVSTLNDEYIVSYGNDNNFAECYIFFNNENSILIKPEKYGNTAAGCYGGTFVKIDENRALFIYSSSQGIYNIHTIYYANY"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A human Fab (IGHV1/IGLV2-Lambda) targeting the Envelope glycoprotein gp120 of Human immunodeficiency virus 1. The gp120 surface protein attaches the virus to the host lymphoid cell by binding to the primary receptor CD4, inducing structural rearrangement that creates a high-affinity binding site for chemokine coreceptors. This antibody is designed as a broadly neutralizing antibody targeting the CD4 receptor binding site (CD4bs), with minimal somatic hypermutations concentrated in CDRH2 and CDRL1 to accommodate N-linked glycans while maintaining neutralization potency and breadth across diverse HIV-1 clades.", "target_protein": "VQLVQSGAQVKKPGASVTVSCTASMHWVRQAPGQGLEWMGWKYAQKFRGRVSMTRDTSIEIFYMELSRLRSDDTAVYYCWGQGTLVTVSSAGYTFTGYHINPFRGGVAREMFDSSADWSPWRGMVA", "metadata": {"pdb_id": "9ehl", "light_chain_seq": "SALTQPASVSGSPGQSITISCTGSSRDVGGFDLVSWYQQHPGKAPKLMIYEVSKRPSGVSNRFSASKSGNTASLTISGLQAEDEADYYCYSYADGVAFGGGTKLTVLGQ", "cdrh1_seq": "GYTFTGYH", "cdrh2_seq": "INPFRGGV", "cdrh3_seq": "AREMFDSSADWSPWRGMVA", "cdrl1_seq": "SRDVGGFDL", "cdrl2_seq": "EVS", "cdrl3_seq": "YSYADGVA", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 113]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9ehm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp120, Human immunodeficiency virus 1", "target_domain": "CD4 receptor binding site (CD4bs)", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibodies against conserved HIV-1 Env epitopes"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 2616, 6914, 12, 20733, 7390, 19, 28961, 15755, 17, 18279, 13, 5133, 1920, 11262, 11424, 16102, 1927, 2616, 13141, 3413, 21, 18, 1920, 16102, 3154, 2213, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1988, 15628, 43, 2149, 17, 5173, 2743, 3200, 1958, 11673, 30435, 3448, 18, 2052, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 4095, 3148, 2743, 3200, 12, 4095, 2083, 13, 16, 1956, 6343, 8548, 13317, 19417, 9421, 1922, 20170, 6951, 1930, 20170, 8053, 1942, 16848, 56, 17, 4624, 15509, 2679, 8231, 14377, 10397, 1930, 22532, 3436, 6445, 3525, 17, 21, 15961, 18, 3], "antigen": ["NLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A human Fab, CIS42 (IGHV7/IGLV2-Lambda), targeting a peptide epitope (peptide 20: ASN-PRO-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP) derived from the Circumsporozoite protein of Plasmodium falciparum. The Circumsporozoite protein is an essential sporozoite protein required for sporozoite migration through the host dermis and infection of host hepatocytes, binding to highly sulfated heparan sulfate proteoglycans on hepatocyte surfaces. This antibody forms a complex with the PfCSP peptide epitope. Please provide the HCDR sequences.", "target_protein": "VQLVQSGSELKKPGASVKVSCKTSMNWVRQAPGQGLEWMGWTYAPGFTGRFVFSFDTSVSTAYLQISSLKAEDTAVYYCWGQGTLVTVSSAGYTFTTYAINTNTGNPARVYSYGVPFDY", "metadata": {"pdb_id": "6b5p", "light_chain_seq": "SVLTQPASVSGSPGQSITISCTATSSNVGSFNLVSWYQHHPGKAPKLIIHEVSKRPSGASNRFSGSKSGNTASLTISGLQAEDEADYYCCSYVGSDTWVFGGGTKLTVLGQ", "cdrh1_seq": "GYTFTTYA", "cdrh2_seq": "INTNTGNP", "cdrh3_seq": "ARVYSYGVPFDY", "cdrl1_seq": "SSNVGSFNL", "cdrl2_seq": "EVS", "cdrl3_seq": "CSYVGSDTWV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 106]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "6b5r", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CIS42", "antibody_format": "Fab", "heavy_subclass": "IGHV7", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Circumsporozoite protein, Plasmodium falciparum", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 2616, 6914, 16, 5848, 6852, 12, 20733, 1020, 1027, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 43, 4207, 10095, 12, 4207, 2036, 30, 15118, 17, 1965, 17, 4138, 17, 1965, 17, 15118, 17, 10527, 17, 15118, 17, 1965, 17, 15118, 17, 2326, 17, 4138, 13, 3595, 2037, 1920, 28868, 2074, 26553, 2213, 1927, 15663, 13098, 18, 1920, 28868, 2074, 26553, 2213, 1977, 1925, 4415, 9130, 26553, 2213, 3414, 1958, 9130, 26553, 5049, 2596, 1920, 4423, 20201, 1930, 2909, 1927, 4423, 9919, 16, 2743, 1942, 3626, 26649, 22024, 8767, 25185, 1990, 14675, 7553, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 14425, 3508, 4207, 10095, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["NPDPNANPNVD"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab, 31.a.83 (IGHV3/IGKV3-Kappa), targeting the Hemagglutinin of Influenza A virus. Hemagglutinin is a class I viral fusion protein that binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and mediates fusion of viral and endosomal membranes to deliver the nucleocapsid into the cytoplasm. The antibody is designed as a broadly protective neutralizing antibody targeting the conserved HA stem epitope, binding within the HA stem domain across group 1 and group 2 influenza A viruses.", "target_protein": "EVQLLESGGGLVQPGESLRVSCAASLSWVRQAPGKGLEWVSAYYADTVKGRFTISRDNSQTTLYLQMNSLRADDTATYYCWGKGTTVTVSSAGFTFRDSAISGNGGATAKDESPPIYNLMPGYYSTYYYMDV", "metadata": {"pdb_id": "7u8l", "light_chain_seq": "EIVMTQSPVTLSVSPGETATLSCRASQSVRSNLAWYQQKPGQAPRLLIYGASTRATDIPARFSGSGSGTEFTLSISSLQSDDFAVYYCQQYNHWLRTFGQGTKLEIRTV", "cdrh1_seq": "GFTFRDSA", "cdrh2_seq": "ISGNGGAT", "cdrh3_seq": "AKDESPPIYNLMPGYYSTYYYMDV", "cdrl1_seq": "QSVRSN", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYNHWLRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 119]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5kaq", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "31.a.83", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": "HA stem", "functional_role": "neutralizing", "evidence_quote": "broadly protective antistem antibody"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 16, 3470, 18, 43, 18, 5893, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 18, 26141, 1977, 43, 2921, 51, 4324, 5289, 2213, 1988, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 10412, 5289, 1927, 4324, 1930, 16514, 5726, 1942, 3971, 1920, 2797, 28712, 1960, 2460, 1920, 5239, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 6337, 12130, 3533, 5133, 1920, 5305, 2118, 4402, 10095, 16, 2743, 2651, 1920, 2118, 4402, 3418, 3436, 2210, 21, 1930, 2210, 22, 7108, 43, 6241, 18, 3], "antigen": ["GIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQI", "ATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICKGKKAVDLGSCGILGTIIGPPQCDLHLEFKADLIIERRNSSDICYPGRFTNEEALRQIIRESGGIDKESMGFRYSGIRTDGATSACKRTVSSFYSEMKWLSSSMNNQVFPQLNQTYRNTRKEPALIVWGVHHSSSLDEQNKLYGTGNKLITVGSSKYQQSFSPSPGARPKVNGQAGRIDFHWMLLDPGDTVTFTFNGAFIAPDRATFLRSNAPSGEYNGKSLGIQSDAQIDESECFTPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPE"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A human Fab (IGHV1/IGKV3-Kappa) targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding. The antibody is designed as a neutralizing antibody capable of blocking ACE2 receptor engagement and suppressing spike-mediated membrane fusion, with maintained potency against the Delta variant (B.1.617 lineage).", "target_protein": "VQLQQSGPELVKPGASVKISCKASMNWMKQSPEKSLEWIGETDNQKFKAKATLTVDKSSSTAYMQLKSLTSEDSAVYYCWGQGTSVTVSKAGYSFTGYSINPSTGGTARSRGDY", "metadata": {"pdb_id": "7mw5", "light_chain_seq": "IVLTQSPASLAVSLGQRATISCRASESVEYYGTSLMQWYQQKPGQPPKVLIYAASNVESGVPARFSGSGSGTDFSLNIHPVEEDDIAMYFCQQSRKVPWTFGGGTKLEIKRT", "cdrh1_seq": "GYSFTGYS", "cdrh2_seq": "INPSTGGT", "cdrh3_seq": "ARSRGDY", "cdrl1_seq": "ESVEYYGTSL", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSRKVPWT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 101]", "cdrl1_pos": "[25, 34]", "cdrl2_pos": "[52, 54]", "cdrl3_pos": "[91, 99]", "cdrh3_split": "val", "cdrh3_cluster": "7mw5", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "potently neutralized SARS-CoV-2 WA1 and B.1.617 pseudoviruses"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 7131, 1927, 7472, 8298, 1028, 3148, 9577, 1930, 13556, 10429, 17, 3434, 3260, 5289, 16, 1956, 5514, 10397, 3316, 1920, 9649, 6031, 12, 44, 18, 21, 18, 5473, 1027, 7924, 13, 18, 3], "antigen": ["CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLSLLIVNNATNVVIKVCEFQFCNDPFLGVYYSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPEL"]} {"modality_type": "antibody", "text": "A synthetic antibody (IGHV3/IGKV1-Kappa) targeting the pH-gated potassium channel KcsA of Streptomyces lividans. The pH-gated potassium channel KcsA acts as a pH-gated potassium ion channel; changing the cytosolic pH from 7 to 4 opens the channel, with monovalent cation preference K(+) > Rb(+) > NH4(+) >> Na(+) > Li(+). This antibody forms a complex with the pH-gated potassium channel KcsA. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "VQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWIGENYADSVKGRFTISATSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGYTFTSDWIIPSYGRAARERGDGYFDY", "metadata": {"pdb_id": "7mub", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSIGTDIHWYQQKPGKAPKLLIKYAESISGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSNRWPFTFGQGTKVEIKRT", "cdrh1_seq": "GYTFTSDW", "cdrh2_seq": "IIPSYGRA", "cdrh3_seq": "ARERGDGYFDY", "cdrl1_seq": "QSIGTD", "cdrl2_seq": "YA", "cdrl3_seq": "QQSNRWPFT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[94, 104]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "7mdj", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "antibody", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "pH-gated potassium channel KcsA, Streptomyces lividans", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 43, 6830, 3533, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 2087, 17, 12336, 9057, 4999, 29971, 1019, 1927, 22874, 15260, 9532, 3355, 18, 1920, 2087, 17, 12336, 9057, 4999, 29971, 1019, 8016, 1966, 43, 2087, 17, 12336, 9057, 4755, 4999, 31, 8546, 1920, 9410, 2087, 2037, 27, 1942, 24, 19851, 1920, 4999, 16, 1956, 28685, 9976, 8308, 53, 12, 15, 13, 34, 6160, 12, 15, 13, 34, 14945, 12, 15, 13, 34, 34, 4049, 12, 15, 13, 34, 2336, 12, 15, 13, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 2087, 17, 12336, 9057, 4999, 29971, 1019, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["CAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVVTATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALATWFVGQC"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A human Fab, CAP228-3D (IGHV5/IGLV6-Lambda), targeting the V1V2 region of the Envelope glycoprotein gp160 of Human immunodeficiency virus 1. The Envelope glycoprotein gp160 attaches the virus to the host lymphoid cell by binding to the primary receptor CD4 and mediates fusion of viral and host cell membranes during entry. The antibody is designed to block the interaction between HIV-1 V2 and the \u03b14\u03b27 integrin, recognizing a helix-coil conformation of V2 that is presented on infected cell surfaces and virion particles.", "target_protein": "EVQLVQSGAEVKKPGESLKISCKGFIAWVRQMPGKGLEWMGMKYSPSLQGQVTISGDKSISTAYLQWSSLKASDTAMYYCWGRGTLVTVSSAGYSFSTYWIYPGDSDTARLLNNYDSSGFLYWYLDL", "metadata": {"pdb_id": "6fy3", "light_chain_seq": "NFMLTQPHSVSESPGKTVTISCTRSSGSIASDYVQWYQQRPGSSPTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDMTNHNWVFGGGTKLTVLGQ", "cdrh1_seq": "GYSFSTYW", "cdrh2_seq": "IYPGDSDT", "cdrh3_seq": "ARLLNNYDSSGFLYWYLDL", "cdrl1_seq": "SGSIASDY", "cdrl2_seq": "EDN", "cdrl3_seq": "QSYDMTNHNWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[91, 101]", "cdrh3_split": "val", "cdrh3_cluster": "6fy3", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CAP228-3D", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGLV6", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus 1", "target_domain": "V1V2 region", "functional_role": "other", "evidence_quote": "block the binding of HIV-1 to \u03b14\u03b27 integrin"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 2853, 24894, 17, 5050, 12, 20733, 1020, 1015, 19, 28961, 25606, 17, 18279, 13, 16, 5133, 1920, 11217, 15755, 3031, 1927, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 21, 18, 1920, 11262, 11424, 4882, 16954, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 1930, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1942, 3367, 1920, 2835, 2192, 3525, 17, 21, 12701, 1930, 1920, 17623, 1110, 1027, 8920, 16, 15667, 43, 7864, 17, 9121, 7748, 1927, 12701, 1988, 1977, 3549, 1990, 4014, 2024, 7553, 1930, 19230, 5569, 18, 3], "antigen": ["RDKKQKAYALFYRPD"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A murine Fab, 3H4 (IGHV1/IGKV14-Kappa), targeting the HLA class I histocompatibility antigen, alpha chain E (HLA-E) in complex with the VL9 leader peptide of Homo sapiens. HLA-E is a non-classical major histocompatibility class Ib molecule that functions as a ligand for the natural killer cell inhibitory receptor NKG2A/CD94, enabling NK cells to tolerate healthy cells. The antibody is designed to enhance NK cell cytotoxicity by blocking the HLA-E-VL9 interaction with the NKG2A/CD94 inhibitory pathway, thereby relieving NK cell suppression and promoting NK-mediated killing of target cells.", "target_protein": "EVQLQESGPELVKPGASVKIPCKASMDWVKQSHGKSLEWIGDIYNQKFKGKATLTVDKSSSTAYMELRSLTSEDTAVYYCWGTGTTVTVSSAGYTFTDYNINPNNGGTARPDYYGSSYGWYFDV", "metadata": {"pdb_id": "7bh8", "light_chain_seq": "DIVITQSPSSMYASLGERVTITCKASQDINSYLSWFQQKPGKSPKTLIYRANRLVDGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPLTFGAGTKLELKRT", "cdrh1_seq": "GYTFTDYN", "cdrh2_seq": "INPNNGGT", "cdrh3_seq": "ARPDYYGSSYGWYFDV", "cdrl1_seq": "QDINSY", "cdrl2_seq": "RAN", "cdrl3_seq": "LQYDEFPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7bh8", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "3H4", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV14", "is_engineered": false, "target_antigen": "HLA class I histocompatibility antigen, alpha chain E with VL9 leader peptide, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "enhanced NK-92 cell cytotoxicity against HLA-E-VL9-expressing target cells by blocking NKG2A/CD94 pathway"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 7135, 6914, 16, 7648, 1006, 12, 20733, 7390, 19, 7021, 1040, 7390, 1006, 17, 12093, 13, 16, 5133, 1920, 7225, 2921, 51, 22836, 4730, 16, 4595, 4659, 47, 12, 7225, 17, 47, 13, 1922, 2796, 1956, 1920, 9920, 1026, 17442, 4207, 1927, 16350, 27974, 18, 7225, 17, 47, 1977, 43, 2447, 17, 8445, 3044, 22836, 2921, 6180, 5388, 1988, 4088, 1966, 43, 5207, 1958, 1920, 4613, 16644, 2024, 5431, 3148, 23633, 1019, 19, 2464, 11226, 16, 12180, 5916, 2094, 1942, 21407, 4097, 2094, 18, 1920, 3533, 1977, 4609, 1942, 4826, 5916, 2024, 8470, 2007, 7472, 1920, 7225, 17, 47, 17, 9920, 1026, 2835, 1956, 1920, 23633, 1019, 19, 2464, 11226, 5431, 3374, 16, 6113, 15058, 3141, 5916, 2024, 6412, 1930, 7356, 5916, 17, 3434, 11879, 1927, 2758, 2094, 18, 3], "antigen": ["GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYWDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDGKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLLHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP", "VMAPRTVLL"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A human Fab, panitumumab (IGHV4/IGKV1-Kappa), targeting the engineered Epidermal growth factor receptor of Homo sapiens. The Epidermal growth factor receptor is a receptor tyrosine kinase that binds ligands of the EGF family and activates multiple downstream signaling cascades including RAS-RAF-MEK-ERK, PI3 kinase-AKT, PLCgamma-PKC, and STATs pathways. The antibody is designed to block EGFR signaling for treatment of metastatic colorectal cancer, with the objective of maintaining binding affinity across EGFR variants including the S468R resistance mutation.", "target_protein": "QVQLQESGPGLVKPSETLSLTCTVSWTWIRQSPGKGLEWIGHNYNPSLKSRLTISIDTSKTQFSLKLSSVTAADTAIYYCWGQGTMVTVSSAGGSVSSGDYYIYYSGNTVRDRVTGAFDI", "metadata": {"pdb_id": "5sx4", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQHFDHLPLAFGGGTKVEIKRT", "cdrh1_seq": "GGSVSSGDYY", "cdrh2_seq": "IYYSGNT", "cdrh3_seq": "VRDRVTGAFDI", "cdrl1_seq": "QDISNY", "cdrl2_seq": "DAS", "cdrl3_seq": "QHFDHLPLA", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5sx5", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "panitumumab", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Epidermal growth factor receptor, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "panitumumab and cetuximab target the epidermal growth factor receptor for the treatment of metastatic colorectal cancer"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 3797, 13378, 6683, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 9844, 2905, 2991, 3148, 1927, 16350, 27974, 18, 1920, 9844, 2905, 2991, 3148, 1977, 43, 3148, 6941, 4016, 1988, 6876, 6908, 1927, 1920, 4451, 3416, 1930, 9094, 3137, 5863, 3197, 15967, 2710, 6520, 17, 12783, 17, 12551, 17, 7770, 16, 21197, 4016, 17, 5496, 16, 12897, 4223, 28262, 17, 8425, 16, 1930, 3156, 1036, 3873, 18, 1920, 3533, 1977, 4609, 1942, 3367, 5775, 3197, 1958, 2311, 1927, 6476, 7820, 2539, 16, 1956, 1920, 4470, 1927, 8231, 2743, 5173, 3436, 5775, 4936, 2710, 1920, 6934, 6735, 1005, 3554, 3979, 18, 3], "antigen": ["KKVCNFKDSLSIDATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLDITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVS"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A murine Fab, huAR9.6 (IGHV5/IGKV3-Kappa), targeting human Mucin-16 (MUC16), a heavily glycosylated protein that provides a protective, lubricating barrier at mucosal surfaces. The antibody is designed to bind a discontinuous epitope within the SEA domain of MUC16 and to engage multiple homologous SEA domains across the tandem repeat region, enabling dense avid binding to MUC16-expressing pancreatic ductal adenocarcinoma cells. The antibody is intended to block MUC16-mediated ErbB and AKT signaling and to confer anti-tumor protection through antibody-dependent cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC).", "target_protein": "VQLVESGGGLVQPGGSRKLSCAASMHWVRQAPEKGLEWVAYYYGDTLQGRFIISRDNPKNTLFLQMTSLRSEDTAMYYCWGQGTSVTVSSAGFTFSTFGISSGSSTIARSGYDYDPIYYALDY", "metadata": {"pdb_id": "8gkl", "light_chain_seq": "DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFMNWFQQKPGHPPKLLIYGASNQGSGVPARFSGSGSGTDFSLNIHPMEEDDAAMYFCQQTKEVPWTFGGGTKVEIKRA", "cdrh1_seq": "GFTFSTFG", "cdrh2_seq": "ISSGSSTI", "cdrh3_seq": "ARSGYDYDPIYYALDY", "cdrl1_seq": "ESVDNYGISF", "cdrl2_seq": "GAS", "cdrl3_seq": "QQTKEVPWT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 110]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "8gkl", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "huAR9.6", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Mucin-16, Homo sapiens", "target_domain": "SEA domain", "functional_role": "other", "evidence_quote": "huAR9.6 blocked MUC16-mediated ErbB and AKT activation and induced ADCC and CDC"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 5897, 1933, 1026, 18, 26, 12, 20733, 1020, 1015, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 2616, 14455, 17, 2641, 12, 21215, 1016, 13, 16, 43, 14231, 17514, 2213, 1988, 4558, 43, 6337, 16, 30391, 2287, 7104, 2019, 9565, 7553, 18, 1920, 3533, 1977, 4609, 1942, 4566, 43, 24736, 10095, 2651, 1920, 9309, 3418, 1927, 21215, 1016, 1930, 1942, 11580, 3137, 8725, 9309, 4682, 3436, 1920, 10361, 6865, 3031, 16, 12180, 10472, 22731, 1007, 2743, 1942, 21215, 1016, 17, 4590, 6356, 15154, 9573, 2094, 18, 1920, 3533, 1977, 11214, 1942, 3367, 21215, 1016, 17, 3434, 11954, 1930, 5496, 3197, 1930, 1942, 7909, 2246, 17, 2798, 6202, 2596, 3533, 17, 3100, 3689, 8470, 12, 25899, 13, 1930, 5508, 17, 3100, 8470, 12, 7137, 13, 18, 3], "antigen": ["PLLVPFTLNFTITNLKYEEDMHCPGSRKFNTTERVLQSLLGPMFKNTSVGPLYSGCRLTLLRSEKDGAATGVDAICTHRDREQLYWELSQLTNGIKELGPYTLDRNSLYVNGFTHQ"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A murine Fab, vFP7.04 (IGHV1/IGKV1-Kappa), targeting the Envelope glycoprotein gp41 of Human immunodeficiency virus 1. The Envelope glycoprotein gp160 is proteolytically cleaved to produce gp120 and gp41, which together mediate viral attachment to host cells and membrane fusion. The antibody is designed as a vaccine-elicited neutralizing antibody targeting the fusion peptide epitope to neutralize diverse HIV-1 strains, binding within the Fusion peptide. Please generate its HCDRs.", "target_protein": "QVQLQQSGAELVRPGASVTLSCKASMHWVKQTPVHGLEWIGAAYTQKFKGKAMLTADKSSSTAYMELRSLTSEDSAVYFCWGTGTTVTVSGYTFTDYEIVPETGFTSRLRLYWYFDV", "metadata": {"pdb_id": "6cue", "light_chain_seq": "GVLMTQSPLSLPVRLGDQASISCRSSQSIVYSNGNTYLEWYLQRPGQSPKLLIYKVSNRFSGVPDRVSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEI", "cdrh1_seq": "GYTFTDYE", "cdrh2_seq": "IVPETGFT", "cdrh3_seq": "SRLRLYWYFDV", "cdrl1_seq": "QSIVYSNGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQGSHVPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "6cdm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "vFP7.04", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp41, Human immunodeficiency virus 1", "target_domain": "Fusion peptide", "functional_role": "neutralizing", "evidence_quote": "vaccine-elicited antibodies that neutralize diverse strains of HIV-1"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 15691, 1034, 1027, 18, 5228, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 25618, 1927, 2616, 13141, 3413, 21, 18, 1920, 11262, 11424, 4882, 16954, 1977, 12712, 2169, 10246, 1942, 5074, 16102, 1930, 25618, 16, 2154, 4084, 8265, 4324, 8576, 1942, 4423, 2094, 1930, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 5955, 17, 9856, 12130, 3533, 5133, 1920, 5289, 4207, 10095, 1942, 25885, 6445, 3525, 17, 21, 4046, 16, 2743, 2651, 1920, 5289, 4207, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A human Fab, SAN27-14 (IGHV1/IGKV1-Kappa), targeting the engineered prefusion-stabilized Fusion glycoprotein F0 of Human metapneumovirus. The Fusion glycoprotein F0 is required for viral entry and is the primary target of neutralizing antibodies. The antibody is designed as a prefusion-specific neutralizing antibody targeting antigenic site V on the apex of the hMPV F protein.", "target_protein": "QVRLEQSGADVKKPGASVRVSCKASIHWVRQAPGQGLEWMGWNYAQTFRGRVTLTRDTSLKTLHLDLISLRSGDTAIYYCWGQGTLVTVSSGYTFNGYYINPYTGETARGNCSISGCYYSWLDH", "metadata": {"pdb_id": "7tjq", "light_chain_seq": "DIQMTQSPSTLSASVGDRVTITCRASQSINTWLAWYQQKPGKAPKLLIYEASSLERGVPSRFSGSGSGTGFTLTISSLQPDDFATYFCQQYNTYPRTFGQGTKVEIK", "cdrh1_seq": "GYTFNGYY", "cdrh2_seq": "INPYTGET", "cdrh3_seq": "ARGNCSISGCYYSWLDH", "cdrl1_seq": "QSINTW", "cdrl2_seq": "EAS", "cdrl3_seq": "QQYNTYPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7tjq", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "SAN27-14", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Fusion glycoprotein F0, Human metapneumovirus", "target_domain": "Antigenic site V", "functional_role": "neutralizing", "evidence_quote": "prefusion-specific neutralizing antibodies targeting the apex of hMPV F"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 2616, 6914, 16, 6867, 4282, 17, 2607, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 9328, 2670, 17, 12017, 5289, 11424, 17930, 1927, 2616, 5880, 27257, 3708, 12492, 11074, 18, 1920, 5289, 11424, 17930, 1977, 3414, 1958, 4324, 6904, 1930, 1977, 1920, 3065, 2758, 1927, 12130, 3788, 18, 1920, 3533, 1977, 4609, 1966, 43, 9328, 2670, 17, 2487, 12130, 3533, 5133, 14606, 3200, 64, 1990, 1920, 14091, 1927, 1920, 5833, 17223, 48, 2213, 18, 3], "antigen": ["LKESYLEESCSTITEGYLSVLRTGWYTNVFTLEVGDVENLTCADGPSLIKTELDLTKSALRELRTVSAFVLGAIACGVATAAAVTAGVAIAKCIRLESEVTAIKNCLKKTNECVSTLGCGVRVLATAVRELKDFVSKNLTRAINKNKCDIPDLKMAVSFSQFNRRFLNVVRQFSDNAGITPAISKDLMTDAELARAISNMPTSAGQIKLMLENRAMVRRKGFGILIGVYGSSVIYMVQLPIFGVIDTPCWIVKAAPSCSEKKGNYACLLREDQGWYCQNAGSTVYYPCEKDCETRGDHVFCDTAAGINVAEQSKECNINISTTNYPCKVSCGRHPISMVALSPLGALVACYKGVSCSIGSNRVGIIKQLNKGCSYITNQDADTVTIDNTVYQLSKVEGEQHVIKGRPVSSSFDPVKFPQDQFNVALDQCFE"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A murine Fv, mAb6D8 (IGHV14/IGKV3-Kappa), targeting the Merozoite surface protein 2 of Plasmodium falciparum. Merozoite surface protein 2 is an intrinsically disordered, membrane-anchored antigen that may play a role in merozoite attachment to the erythrocyte. The antibody is designed to recognize a conserved N-terminal epitope of MSP2 on the parasite surface, with the understanding that this epitope undergoes conformational masking through lipid-mediated disorder-to-order transitions that restrict antibody accessibility on the native merozoite. Can you generate its HCDRs?", "target_protein": "QVQLQQSGDELVKPGASVKLSCTVSIHWMKQRPEQGLEWIGRKYAPKFQDKATMTADTSSNTAYLQLSSLASEDAAVYYCWGQGTLVTVSAGFNIKDDFIDPANGYTATYGVAY", "metadata": {"pdb_id": "4qyo", "light_chain_seq": "DIVLTQSPASLAVSLGQRATISCKASQSVDHDGDSYMNWFQQKPGQSPKLLIYAASNLESGIPARFSGSGSGTDFTLNIHPVEEEDAATYYCQQTNEDPYTFGGGTKLEIK", "cdrh1_seq": "GFNIKDDF", "cdrh2_seq": "IDPANGYT", "cdrh3_seq": "ATYGVAY", "cdrl1_seq": "QSVDHDGDSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQTNEDPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 102]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "4r3s", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "mAb6D8", "antibody_format": "Fv", "heavy_subclass": "IGHV14", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Merozoite surface protein 2, Plasmodium falciparum", "target_domain": null, "functional_role": "other", "evidence_quote": "antibodies able to recognize the N-terminal region of MSP2 on the merozoite surface"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 7135, 11417, 16, 7032, 1016, 1007, 1025, 12, 20733, 7390, 1006, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 6902, 26553, 3154, 2213, 22, 1927, 15663, 13098, 18, 6902, 26553, 3154, 2213, 22, 1977, 1925, 20061, 13885, 16, 3260, 17, 17199, 4730, 1988, 2278, 3918, 43, 2770, 1922, 6902, 26553, 8576, 1942, 1920, 15469, 18, 1920, 3533, 1977, 4609, 1942, 9967, 43, 5305, 56, 17, 4262, 10095, 1927, 22064, 1028, 1990, 1920, 8652, 3154, 16, 1956, 1920, 4339, 1988, 2052, 10095, 14928, 8523, 20116, 2596, 4486, 17, 3434, 4770, 17, 1942, 17, 3238, 10673, 1988, 18240, 3533, 12995, 1990, 1920, 6196, 6902, 26553, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["NAYNMSIRR"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human Fab, ADI-15878 (IGHV3/IGKV1-Kappa), targeting the engineered trimeric Envelope glycoprotein of Zaire ebolavirus (Makona variant, mucin-deleted). The Envelope glycoprotein mediates viral entry through receptor binding and membrane fusion, and is downregulated by the virus to evade immune surveillance. The antibody is designed as a pan-ebolavirus neutralizing antibody that engages conserved structural elements of the trimeric spike, preventing viral entry and conferring protection across the ebolavirus genus. What would the HCDRs be?", "target_protein": "QVQLVQSGVTLVQPGGSLRVSCAASMSWVRQAPGKGLEWVSAYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGALVTVSGFTFSSYAISGLGGSTAKDHRVWAAGYHFDY", "metadata": {"pdb_id": "6dzl", "light_chain_seq": "DIVLTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGEAPKLLISDASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYYSSPTFGGGTKVEIK", "cdrh1_seq": "GFTFSSYA", "cdrh2_seq": "ISGLGGST", "cdrh3_seq": "AKDHRVWAAGYHFDY", "cdrl1_seq": "QSISSW", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYYSSPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6dzm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ADI-15878", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Envelope glycoprotein, Zaire ebolavirus", "target_domain": "Internal fusion loop and heptad repeat 1 (HR1)", "functional_role": "neutralizing", "evidence_quote": "potent human survivor-derived antibody ADI-15878, which has full pan-ebolavirus activity and has shown protection in three stringent animal models"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 6914, 16, 2041, 1033, 17, 14340, 7950, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 29177, 11262, 11424, 1927, 26112, 2952, 24497, 11074, 12, 4340, 12502, 6031, 16, 14455, 17, 11782, 13, 18, 1920, 11262, 11424, 10412, 4324, 6904, 2596, 3148, 2743, 1930, 3260, 5289, 16, 1930, 1977, 9936, 2007, 1920, 3413, 1942, 28917, 3743, 7889, 18, 1920, 3533, 1977, 4609, 1966, 43, 3797, 17, 24497, 11074, 12130, 3533, 1988, 11580, 1036, 5305, 4346, 5362, 1927, 1920, 29177, 10429, 16, 8444, 4324, 6904, 1930, 21510, 6202, 3436, 1920, 24497, 11074, 9487, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["PKCNPNLHFWTTQDEGAAIGLAWIPYFGPAAEGIYTEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRW", "SIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSVTKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYASG"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A murine Fab (IGHV3/IGKV4-Kappa) targeting the Voltage-gated potassium channel (KvAP) of Aeropyrum pernix. The Voltage-gated potassium channel mediates voltage-dependent potassium ion permeability and forms a potassium-selective channel through which potassium ions pass in accordance with their electrochemical gradient. This antibody is intended as a structural tool to stabilize and facilitate crystallographic characterization of the voltage-sensor domain.", "target_protein": "DVQLQESGPGLVKPSQSLSLTCTVTWNWIRQFPGNKLEWMGYSYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYFCWGQGTSVTVSSAGYSITNNYAINYSGTTVRGYDYFAMDY", "metadata": {"pdb_id": "1ors", "light_chain_seq": "QIVLTQSPAIMSASLGDRVTMTCTASSSVSSSYLHWYQQKPGSSPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSMEAEDAATYYCHQFHRSLTFGSGTKLEIKRA", "cdrh1_seq": "GYSITNNYA", "cdrh2_seq": "INYSGTT", "cdrh3_seq": "VRGYDYFAMDY", "cdrl1_seq": "SSVSSSY", "cdrl2_seq": "STS", "cdrl3_seq": "HQFHRSLT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "1ors", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Voltage-gated potassium channel, Aeropyrum pernix", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "crystal structure of the full-length channel and isolated voltage-sensor domain in complex with monoclonal Fab fragments"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 7135, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1920, 6889, 17, 12336, 9057, 4999, 12, 10674, 2026, 13, 1927, 6049, 13518, 1989, 2079, 8635, 1039, 18, 1920, 6889, 17, 12336, 9057, 4999, 10412, 6889, 17, 3100, 9057, 4755, 8828, 1930, 4952, 43, 9057, 17, 5328, 4999, 2596, 2154, 9057, 6982, 4675, 1922, 7488, 1956, 2310, 13197, 6494, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 1930, 6628, 17832, 7285, 1927, 1920, 6889, 17, 6443, 3418, 18, 3], "antigen": ["DVMEHPLVELGVSYAALLSVIVVVVEYTMQLSGEYLVRLYLVDLILVIILWADYAYRAYKSGDPAGYVKKTLYEIPALVPAGLLALIEGHLAGLGLFRLVRLLRFLRILLIISRGSKFLSAIADAADKLVPR"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A murine Fab, 2411a (IGHV1/IGKV3-Kappa), targeting the engineered HIV-1 gp120 core of Human immunodeficiency virus 1. The gp120 surface protein attaches the virus to the host lymphoid cell by binding to the primary receptor CD4, inducing structural rearrangement that creates a high-affinity binding site for chemokine coreceptors. The antibody is designed as a broadly neutralizing antibody of the VRC01-class, targeting the CD4 receptor binding site (CD4bs), with the objective of penetrating the glycan276 shield present on most circulating HIV-1 strains to achieve broad neutralization across diverse viral variants.", "target_protein": "QVQLVQSGAEMKKPGASVRVSCEASLHWMRQAPGQGIEWLGWNYAHKFQGRVSMTRDTSIDTAYLELINLRSDDTAIYYCWGQGTLVSVSSAGYTFTDYVIKPRYGAVARSFDSDYEWWFTY", "metadata": {"pdb_id": "7jks", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASYFISRDYLAWYQQRPGQAPKLLIYGTTTRASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYEFFGLGTKVEIKRT", "cdrh1_seq": "GYTFTDYV", "cdrh2_seq": "IKPRYGAV", "cdrh3_seq": "ARSFDSDYEWWFTY", "cdrl1_seq": "YFISRDY", "cdrl2_seq": "GTT", "cdrl3_seq": "QQYEF", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 93]", "cdrh3_split": "val", "cdrh3_cluster": "7jks", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2411a", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "HIV-1 gp120 core, Human immunodeficiency virus 1", "target_domain": "CD4 receptor binding site (CD4bs)", "functional_role": "neutralizing", "evidence_quote": "vaccine-elicited broadly neutralizing VRC01-class antibody capable of neutralizing viruses bearing glycan276"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 7135, 6914, 16, 21616, 6146, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 3525, 17, 21, 16102, 4728, 1927, 2616, 13141, 3413, 21, 18, 1920, 16102, 3154, 2213, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1988, 15628, 43, 2149, 17, 5173, 2743, 3200, 1958, 11673, 30435, 3448, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1927, 1920, 12110, 1030, 6924, 17, 2921, 16, 5133, 1920, 4095, 3148, 2743, 3200, 12, 4095, 2083, 13, 16, 1956, 1920, 4470, 1927, 19879, 1920, 15060, 25085, 19397, 2481, 1990, 2501, 7396, 3525, 17, 21, 4046, 1942, 6230, 4949, 14377, 3436, 6445, 4324, 4936, 18, 3], "antigen": ["WKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKIIIVQLNETVEINCTRPNIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNNINITLPCRIKQIINMWQEVGKAMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIE"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A human Fab, CH03 (IGHV3/IGKV3-Kappa), targeting the V1V2 domain of Envelope glycoprotein gp160 from Human immunodeficiency virus type 1. The Envelope glycoprotein gp160 oligomerizes into trimers and is proteolytically cleaved to produce gp120, which attaches the virus to host lymphoid cells by binding to the primary receptor CD4, inducing structural rearrangement that creates high-affinity binding sites for chemokine coreceptors. The antibody is designed as a broadly neutralizing antibody targeting the V1V2 domain, which presents a quaternary epitope.", "target_protein": "EVQLVESGGGVVRPGGSLRLSCAASLTWVRQVPGKGLHWVSGRYADSVRGRFSMSRDNSNNIAYLQMKNLRVDDTALYYCWGRGTLVTVSSAGFIFENYGMNWNGGDTARGTDYTIDDQGIFYKGSGTFWYFDL", "metadata": {"pdb_id": "5esv", "light_chain_seq": "EIVLTQSPATLSLSPGERATLSCRASQSVHPKYFAWYQQKPGQSPRLLIYSGSTRAAGIADRFSGGGSGIHFTLTITRVEPEDFAVYFCQQYGGSPYTFGQGTKVELRRT", "cdrh1_seq": "GFIFENYG", "cdrh2_seq": "MNWNGGDT", "cdrh3_seq": "ARGTDYTIDDQGIFYKGSGTFWYFDL", "cdrl1_seq": "QSVHPKY", "cdrl2_seq": "SGS", "cdrl3_seq": "QQYGGSPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 121]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "5esz", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CH03", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus type 1", "target_domain": "V1V2", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibodies (bNAbs) against HIV-1-Env V1V2"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 2616, 6914, 16, 2016, 12962, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11217, 15755, 3418, 1927, 11262, 11424, 4882, 16954, 2037, 2616, 13141, 3413, 2601, 21, 18, 1920, 11262, 11424, 4882, 16954, 13034, 4517, 2460, 28220, 1930, 1977, 12712, 2169, 10246, 1942, 5074, 16102, 16, 2154, 5823, 1918, 1920, 3413, 1942, 4423, 11751, 2094, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1988, 15628, 2149, 17, 5173, 2743, 3402, 1958, 11673, 30435, 3448, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 11217, 15755, 3418, 16, 2154, 8178, 43, 21920, 10095, 18, 3], "antigen": ["SLIRIGHGFDVHAFGCVTLNCSDAKVNINTREEIKNCSFNATTELRDKKKKEYALFYRLDIVPLNSEYRLINCNSGGDVALHALTDAILGAAALGDIGKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTQEGIACEAVALLIRQGLEV"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A murine Fab, 2C11 (IGHV1/IGKV12-Kappa), targeting the engineered Protein-serine O-palmitoleoyltransferase porcupine (isoform 2) of Homo sapiens. Porcupine is a key regulator of the Wnt signaling pathway that mediates the attachment of palmitoleate to Wnt proteins, a modification required for efficient binding to frizzled receptors. The antibody is designed as a structural tool to enable cryo-EM visualization of PORCN in complex with substrates and inhibitors, binding to the cytosolic region without interfering with enzymatic activity.", "target_protein": "EIQLQQSGAELVKPGASVKMSCKVSMNWVKQSHGKSLEWIGNNYNQKFTGKATFTVDRSSSTAYMQLDSLTSEDSAVYYCWGQGTLVTVSSGYSFTGYNINPYYVSTARSYGSSHTFAY", "metadata": {"pdb_id": "7ure", "light_chain_seq": "DIHMTQSPASLSAFVGETVTITCRTSENIFSYLAWYQQKQGKSPQLLVYNAKTLTSGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGSPYTFGGGTKLEIK", "cdrh1_seq": "GYSFTGYN", "cdrh2_seq": "INPYYVST", "cdrh3_seq": "ARSYGSSHTFAY", "cdrl1_seq": "ENIFSY", "cdrl2_seq": "NAK", "cdrl3_seq": "QHHYGSPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7ura", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2C11", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV12", "is_engineered": true, "target_antigen": "Protein-serine O-palmitoleoyltransferase porcupine, Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "monoclonal antibody denoted 2C11 that explicitly binds to native PORCN...to capture the substrate-bound state"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 6921, 3242, 12, 20733, 7390, 19, 7021, 1040, 7390, 1028, 17, 12093, 13, 16, 5133, 1920, 11091, 2213, 17, 8468, 57, 17, 13615, 2456, 10921, 9961, 4572, 18021, 12184, 12, 6174, 22, 13, 1927, 16350, 27974, 18, 4572, 18021, 12184, 1977, 43, 3834, 7888, 1927, 1920, 7028, 3197, 3374, 1988, 10412, 1920, 8576, 1927, 13615, 2456, 2010, 1942, 7028, 2697, 16, 43, 6295, 3414, 1958, 5807, 2743, 1942, 9081, 18559, 2824, 4086, 18, 1920, 3533, 1977, 4609, 1966, 43, 4346, 5229, 1942, 8675, 15822, 17, 2391, 9966, 1927, 4572, 7814, 1922, 2796, 1956, 6249, 1930, 4472, 16, 2743, 1942, 1920, 9410, 3031, 2979, 13369, 1956, 8145, 2455, 18, 3], "antigen": ["FSRQEFFQQLLQGCLLPTAQQGLDQIWLLLAICLACRLLWRLGLPSYLKHASTVAGGFFSLYHFFQLHMVWVVLLSLLCYLVLFLCRHSSHRGVFLSVTILIYLLMGEMHMVDTVTWHKMRGAQMIVAMKAVSLGFDLDRGEVGTVPSPVEFMGYLYFVGTIVFGPWISFHSYLQAVQGRPLSCRWLQKVARSLALALLCLVLSTCVGPYLFPYFIPLNARWLRAYESAVSFHFSNYFVGFLSEATATLAGAGFTEEKDHLEWDLTVSKPLNVELPRSMVEVVTSWNLPMSYWLNNYVFKNALRLGTFSAVLVTYAASALLHGFSFHLAAVLLSLAFITYVEHVLRKRLARILSACVLSKRCPPDCSHQHRLGLGVRALNLLFGALAIFHLAYLGSLFDVYGMAYTVHKWSELSWASHWVTFGCWIFYRLIG"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A murine Fab, YN69083 (IGHV1/IGKV4-Kappa), targeting the Solute carrier family 10 member a1 (Hepatic sodium/bile acid cotransporter) of Macaca fascicularis. The hepatic sodium/bile acid cotransporter plays a key role in the enterohepatic circulation of bile salts, transporting conjugated bile acids from plasma into the hepatocyte in a sodium-dependent manner. This antibody is intended as a structural tool to facilitate cryo-EM structural determination of the macaque NTCP protein. Can you generate its HCDRs?", "target_protein": "EVQLQQPGAELVKPGASVKLSCKTSMKWVKQRPGQGLEWIGENYNGKFKSKASLTVDKSSSTAYMQLSSLTSEDSAVYYCWGLGTSVTVSSAGYTFTNYWINPSNGGTTILVYDAYYVFAMDY", "metadata": {"pdb_id": "8xcd", "light_chain_seq": "DIVMTQSPAIMSASPGQKVTITCSASSSVNYMHWYQQKLGSSPKLWIYDTSKLALGVPARFSGSGSGTSYSLTISSMEAEDAASYFCHQWSSYPRTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTNYW", "cdrh2_seq": "INPSNGGT", "cdrh3_seq": "TILVYDAYYVFAMDY", "cdrl1_seq": "SSVNY", "cdrl2_seq": "DTS", "cdrl3_seq": "HQWSSYPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "7fci", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "YN69083", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Solute carrier family 10 member a1 (Hepatic sodium/bile acid cotransporter), Macaca fascicularis", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "mNTCP was complexed with a Fab fragment antibody used in structural studies"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 7135, 6914, 16, 67, 1022, 7093, 13895, 1010, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 16, 5133, 1920, 19661, 9685, 3416, 2119, 7210, 8080, 12, 6095, 5227, 19, 9619, 2687, 14817, 24095, 13, 1927, 13421, 3375, 29990, 18021, 5148, 13950, 18, 1920, 6095, 5227, 19, 9619, 2687, 14817, 24095, 5705, 43, 3834, 2770, 1922, 1920, 5553, 28600, 2479, 9255, 1927, 9619, 16028, 16, 27038, 6765, 9619, 4576, 2037, 3582, 2460, 1920, 14675, 1922, 43, 5227, 17, 3100, 5222, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 6628, 15822, 17, 2391, 4346, 7063, 1927, 1920, 20533, 5891, 10020, 2213, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["RPTDLALSIILVFMLFFVMLSLGCTMEFSKIKAHLWKPKGLAIALVAQYGIMPLTAFVLGKVFQLNNIEALAILVCGCSPGGNLSNVFSLAMKGDMNLSIVMTTCSTFCALGMMPLLLYLYTRGIYDGDLKDKVPYGRIILSLVPVLIPCTIGIVLKSKRPQYMRYVIKGGMIIILLCSVAVTVLSAINVGKSIMFAMTPLLIATSSLMPFIGFLLGYVLSALFCLNGRCRRTVSMETGCQNVQLCSTILNVAFPPEVIGPLFFFPLLYMIFQLGEGLLLIAMFRCYEKF"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A murine Fab, 8E3 (IGHV2/IGLV3-Lambda), targeting Protein A27 of Vaccinia virus. Protein A27 is a structural protein involved in the envelopment of mature virion to form the wrapped virion and participates in mature virion movement within the infected cell. This antibody forms a complex with a linear peptide epitope (residues 101\u2013110) of Protein A27.", "target_protein": "QVQLKQSGPGLVQPSQSLSITCTVSVHWVRQSPGKGLEWLGVDYNAAFISRLSISKDNSKNQVFFKMNSLRADDTAIYYCWGQGTLVTVSAAGLSLTSYGIWSGGNTAIYYRYGAY", "metadata": {"pdb_id": "5eor", "light_chain_seq": "QLVLTQSSSASFSLGASAKLTCTLSSQHSTYTIDWYQQQPLKPPKYVMELRRDGSHNTGDGIPDRFSGSSSGADRYLSISNIQPEDEAIYICGVGDTIKEQFVYVFGGGTKVTVLGQ", "cdrh1_seq": "GLSLTSYG", "cdrh2_seq": "IWSGGNT", "cdrh3_seq": "AIYYRYGAY", "cdrl1_seq": "SQHSTYT", "cdrl2_seq": "LRRDGSH", "cdrl3_seq": "GVGDTIKEQFVYV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 103]", "cdrl1_pos": "[25, 31]", "cdrl2_pos": "[49, 55]", "cdrl3_pos": "[92, 104]", "cdrh3_split": "val", "cdrh3_cluster": "5eor", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "8E3", "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "Protein A27, Vaccinia virus", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 29252, 1010, 12, 20733, 15755, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 5133, 2213, 26293, 1927, 24331, 3413, 18, 2213, 26293, 1977, 43, 4346, 2213, 3286, 1922, 1920, 9840, 2017, 1927, 6665, 19230, 1942, 2386, 1920, 29233, 19230, 1930, 17241, 1922, 6665, 19230, 5829, 2651, 1920, 4014, 2024, 18, 2052, 3533, 4952, 43, 2796, 1956, 43, 4258, 4207, 10095, 12, 4248, 9447, 229, 8139, 13, 1927, 2213, 26293, 18, 3], "antigen": ["VQTGRRPYE"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human Fab, ZK2B10 (IGHV1/IGLV1-Lambda), targeting the ZIKV structural protein E of Zika virus. The envelope glycoprotein E mediates fusion of viral and host cell membranes during entry. The antibody is designed as a neutralizing antibody that prevents membrane fusion by blocking steps between the formation of the fusion intermediate and membrane merger, binding within Domain III (DIII) at the lateral ridge.", "target_protein": "EVQLVQSGAEVKKPGASVKVSCKASINWVRQATGQGLEWMGWGYAQKFQGRVTMTRNTSINTAYMELSSLRSEDTAVYYCWGQGTTVTVSSAGYTFTSGHTFPSYDMNPNRGNTARVRSGTNYGSYYYYYYGMDV", "metadata": {"pdb_id": "6jfi", "light_chain_seq": "SYELTQPPSASGTPGQRVTISCSGSSSNIGNNYVHWYQQLPGSAPKLLIYRNNQRPSGVPDRFSGSKSGTSGSLAISGLRSEDEADYYCASWDDSLSGHWVFGGGTKVTVLGQ", "cdrh1_seq": "GYTFTSGHTFPSYD", "cdrh2_seq": "MNPNRGNT", "cdrh3_seq": "ARVRSGTNYGSYYYYYYGMDV", "cdrl1_seq": "SSNIGNNY", "cdrl2_seq": "RNN", "cdrl3_seq": "ASWDDSLSGHWV", "cdrh1_pos": "[25, 38]", "cdrh2_pos": "[56, 63]", "cdrh3_pos": "[102, 122]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 100]", "cdrh3_split": "val", "cdrh3_cluster": "6jfi", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ZK2B10", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "ZIKV structural protein E, Zika virus", "target_domain": "Domain III (DIII)", "functional_role": "neutralizing", "evidence_quote": "capable of protection against Zika virus infection; functions at steps between fusion intermediate and membrane fusion"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 6914, 16, 68, 6779, 5090, 1008, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 17359, 4346, 2213, 47, 1927, 28593, 3413, 18, 1920, 11262, 11424, 47, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 10299, 3260, 5289, 2007, 7472, 5983, 2192, 1920, 3337, 1927, 1920, 5289, 6129, 1930, 3260, 27399, 1005, 16, 2743, 2651, 3418, 4337, 12, 26028, 1033, 13, 2019, 1920, 5347, 19826, 18, 3], "antigen": ["IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTA"]} {"modality_type": "antibody", "text": "I want an antibody that has the function: A human Fab, 1710 (IGHV3/IGLV3-Lambda), targeting the engineered Circumsporozoite protein of Plasmodium falciparum. The Circumsporozoite protein is essential for sporozoite development, migration, and infection of host hepatocytes through binding to highly sulfated heparan sulfate proteoglycans on hepatocyte surfaces. The antibody is designed to engage the TSP type-1 domain, specifically targeting a polymorphic region that overlaps T cell epitopes. Output the HCDRs.", "target_protein": "EVQLQESGGGLVKPGGSLRLSCAASMNWVRQAPGKGLEWVSSYYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTFSSYSITSSSSYIARDPGIAAADNHWFDP", "metadata": {"pdb_id": "6b0s", "light_chain_seq": "YELTQPPSVSVSPGQTASITCSGDKLGDKYACWYQQKPGQSPVVVIYQDTKRPSGIPERFSGSNSGNTATLTISGTQAMDEADYYCQAWDSSTVVFGGGTKLTVLGQ", "cdrh1_seq": "GFTFSSYS", "cdrh2_seq": "ITSSSSYI", "cdrh3_seq": "ARDPGIAAADNHWFDP", "cdrl1_seq": "KLGDKY", "cdrl2_seq": "QDT", "cdrl3_seq": "QAWDSSTVV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "6b0s", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "1710", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV3", "is_engineered": true, "target_antigen": "Circumsporozoite protein, Plasmodium falciparum", "target_domain": "TSP type-1", "functional_role": "other", "evidence_quote": "antibody interacts with a polymorphic region overlapping two T cell epitopes"}}}, "tokenized_instruction": [2, 51, 12914, 1925, 3533, 1988, 2258, 1920, 2347, 30, 43, 2616, 6914, 16, 16485, 1008, 12, 20733, 1020, 1010, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 5133, 1920, 11091, 28868, 2074, 26553, 2213, 1927, 15663, 13098, 18, 1920, 28868, 2074, 26553, 2213, 1977, 4415, 1958, 9130, 26553, 2740, 16, 5049, 16, 1930, 2909, 1927, 4423, 9919, 2596, 2743, 1942, 3626, 26649, 22024, 8767, 25185, 1990, 14675, 7553, 18, 1920, 3533, 1977, 4609, 1942, 11580, 1920, 14733, 2601, 17, 21, 3418, 16, 4475, 5133, 43, 14240, 3031, 1988, 19853, 62, 2024, 11427, 18, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["EPSDKHIKEYLNKIQNSLSTEWSPCSVTCGNGIQVRIKPGSANKPKDELDYANDIEKKICKMEKC"]} {"modality_type": "antibody", "text": "I want an antibody that has the function: A human Fab, H014 (IGHV1/IGKV6-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors (primarily ACE2) to initiate infection, and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that prevents attachment of SARS-CoV-2 to its host cell receptors by engaging a conformational epitope accessible when the receptor-binding domain is in the open state. Output the HCDRs.", "target_protein": "VQLVQSGAEVKKPGATVKISCKVSIHWVKQAPGKSLEWIGYSDNLKFKGAATLTADTSTDTAYMELSSLRSEDTAVYYCWGQGTTVTVSSAGYSFSNYYIDPFNGGTARSEYDPYYVMDY", "metadata": {"pdb_id": "7cai", "light_chain_seq": "IVLTQSPFQSVSPKEKVTITCRASQSISSNLHWYQQKPDQSPKLLIKYASQSISGIPSRFSGSGSGTDFTLTINSLEAEDFGIYFCQQTNFWPYIFGQGTKLEILKR", "cdrh1_seq": "GYSFSNYY", "cdrh2_seq": "IDPFNGGT", "cdrh3_seq": "ARSEYDPYYVMDY", "cdrl1_seq": "QSISSN", "cdrl2_seq": "YAS", "cdrl3_seq": "QQTNFWPYI", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 107]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "7cak", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "H014", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "efficiently neutralizes SARS-CoV-2 and prevents attachment to host cell receptors"}}}, "tokenized_instruction": [2, 51, 12914, 1925, 3533, 1988, 2258, 1920, 2347, 30, 43, 2616, 6914, 16, 29161, 3745, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 12, 5985, 8298, 1028, 13, 1942, 11051, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 10299, 8576, 1927, 20466, 17, 6083, 17, 22, 1942, 2496, 4423, 2024, 4086, 2007, 15888, 43, 8523, 10095, 10551, 2469, 1920, 3148, 17, 2743, 3418, 1977, 1922, 1920, 4437, 3360, 18, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["PPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab, 2G7 (IGHV1/IGKV1-Kappa), targeting the Glutamate receptor ionotropic, NMDA 1 (GluN1 subunit) of Homo sapiens. GluN1 is a component of N-methyl-D-aspartate receptors that function as heterotetrameric, ligand-gated cation channels participating in synaptic plasticity for learning and memory formation. The antibody is derived from a patient with autoimmune encephalitis and is designed to bind the N-terminal domain of GluN1, inducing chronic downregulation of surface NMDAR density and synaptic function through receptor internalization.", "target_protein": "QVQLVQSGAEVRKPGASVKVSCRASVHWVRQAPGQGLEWLGWDYSQKFQGRVTMTRDTSITTAYVELSSLISDDTAVYYCWGQGTLVTVSSAGYSFTGYYINPNTGGTARDATGAASSPFDY", "metadata": {"pdb_id": "8jj1", "light_chain_seq": "DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQRPGQAPKLLIYMASTLQTGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHYKSYSFGPGTKVDIKR", "cdrh1_seq": "GYSFTGYY", "cdrh2_seq": "INPNTGGT", "cdrh3_seq": "ARDATGAASSPFDY", "cdrl1_seq": "QSISSW", "cdrl2_seq": "MAS", "cdrl3_seq": "QHYKSYS", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 94]", "cdrh3_split": "val", "cdrh3_cluster": "8jj2", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2G7", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Glutamate receptor ionotropic, NMDA 1, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "auto-mAbs induced the downregulation of synaptic NMDARs, without causing a tonic effect on channel activity, indicating that receptor internalization represents a major pathogenic mechanism"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 16424, 1027, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 7627, 3148, 4755, 8405, 16, 10976, 21, 12, 19524, 1009, 5903, 13, 1927, 16350, 27974, 18, 19524, 1009, 1977, 43, 4594, 1927, 56, 17, 4963, 17, 46, 17, 12878, 4086, 1988, 2347, 1966, 19732, 28959, 17118, 16, 5207, 17, 12336, 9976, 5628, 9505, 1922, 6251, 8771, 1958, 4809, 1930, 4525, 3337, 18, 1920, 3533, 1977, 3595, 2037, 43, 2774, 1956, 8904, 18744, 1930, 1977, 4609, 1942, 4566, 1920, 56, 17, 4262, 3418, 1927, 19524, 1009, 16, 7834, 3724, 9894, 1927, 3154, 17585, 3824, 1930, 6251, 2347, 2596, 3148, 12071, 18, 3], "antigen": ["KIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSLTLSSAMWFSWGVLLNSGIGSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQTFENMAGVFMLVAGGIVAGIFLIFIEIAY"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A human Fab (IGHV1/IGKV3-Kappa) targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2, binding within the Receptor-binding domain (RBD). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes during entry. This antibody is designed as a neutralizing antibody with resistance to viral escape and breadth across sarbecovirus lineages, targeting either a conserved core RBD epitope or the receptor-binding motif with functional constraint against escape mutations. Please generate its HCDRs.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7r6w", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibodies with exceptional sarbecovirus breadth and resistance to SARS-CoV-2 escape"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2409, 6904, 18, 2052, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1956, 3554, 1942, 4324, 11781, 1930, 22532, 3436, 9851, 12409, 7414, 10439, 16, 5133, 3108, 43, 5305, 4728, 25780, 10095, 2014, 1920, 3148, 17, 2743, 5219, 1956, 3183, 15309, 3316, 11781, 3527, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A murine Fab, M8a-6 (IGHV1/IGKV6-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the host cell membrane by interacting with host receptors, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting a conserved class 1/4 epitope on the receptor-binding domain to prevent receptor engagement and viral entry.", "target_protein": "QVQLQQPGTELVMPGASVKLSCKTSMHWVKQRPGEGLEWIGEKYNQKFKGKSTLSVDRSSSTAYMQLSSLTSEDSAVYFCWGQGTSLTVSGYTFTHYWIAPSDNYVARPDNSGYPVYFDY", "metadata": {"pdb_id": "7uz5", "light_chain_seq": "DIVMTQSQKFMSTSLGDRVSISCKASQDVGTTVAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGTGSGTDYTLTISSVAAEDLALYYCQQHYNTPYTFGGGTKLEI", "cdrh1_seq": "GYTFTHYW", "cdrh2_seq": "IAPSDNYV", "cdrh3_seq": "ARPDNSGYPVYFDY", "cdrl1_seq": "QDVGTT", "cdrl2_seq": "WAS", "cdrl3_seq": "QQHYNTPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7uz5", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "M8a-6", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody elicited by mosaic-8 RBD-nanoparticle vaccine"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 7135, 6914, 16, 55, 16269, 17, 26, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 43, 5305, 2921, 21, 19, 24, 10095, 1990, 1920, 3148, 17, 2743, 3418, 1942, 4625, 3148, 9577, 1930, 4324, 6904, 18, 3], "antigen": ["YTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A murine Fab, Ky15.10 (IGHV3/IGKV1-Kappa), targeting the Circumsporozoite protein of Plasmodium falciparum (isolate NF54). The Circumsporozoite protein is an essential sporozoite protein required for migration through the host dermis and infection of host hepatocytes, binding to highly sulfated heparan sulfate proteoglycans on hepatocyte surfaces. The antibody is designed as a neutralizing antibody that inhibits sporozoite traversal and parasite liver invasion, adopting a 1210-like binding mode that recognizes the (N/D)PNANPN(A/V) core epitope with cross-reactivity to junctional and repeat peptides. What would the HCDRs be?", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQVPGKGLEWVAIYYADSVKGRFSVSRDNSENTLYLQMSNLRAEDTAVYYCWGQGTTVTVSSAGFTFSNSGIWYDGSNKVRAYFDSENLYDYYGMDV", "metadata": {"pdb_id": "8fa6", "light_chain_seq": "DIQMTQSPSTLSASVGDRVTITCRASQSISRWLAWFQKKPGKAPKLLIYTASNLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYYNYWTFGQGTKVEVKRT", "cdrh1_seq": "GFTFSNSG", "cdrh2_seq": "IWYDGSNK", "cdrh3_seq": "VRAYFDSENLYDYYGMDV", "cdrl1_seq": "QSISRW", "cdrl2_seq": "TAS", "cdrl3_seq": "QQYYNYWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "8fa6", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Ky15.10", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Circumsporozoite protein, Plasmodium falciparum (isolate NF54)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "effectively inhibited Pf sporozoite traversal in vitro and reduced parasite liver load in vivo"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 7135, 6914, 16, 13995, 3962, 18, 2119, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 28868, 2074, 26553, 2213, 1927, 15663, 13098, 12, 9158, 4651, 5651, 13, 18, 1920, 28868, 2074, 26553, 2213, 1977, 1925, 4415, 9130, 26553, 2213, 3414, 1958, 5049, 2596, 1920, 4423, 20201, 1930, 2909, 1927, 4423, 9919, 16, 2743, 1942, 3626, 26649, 22024, 8767, 25185, 1990, 14675, 7553, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7042, 9130, 26553, 27480, 1923, 1930, 8652, 3568, 6254, 16, 20478, 43, 11844, 1008, 17, 3189, 2743, 5754, 1988, 16197, 1920, 12, 56, 19, 46, 13, 21439, 6708, 1022, 12, 43, 19, 64, 13, 4728, 10095, 1956, 3567, 17, 8229, 1942, 21226, 1930, 6865, 5320, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["VDPNANPNV"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A human Fab, DENV-290 (IGHV3/IGKV2-Kappa), targeting the Envelope protein of Dengue virus type 3. The Envelope protein is a component of the viral RNA replication complex that functions in virion assembly and antagonizes the host immune response. The antibody is designed as a neutralizing antibody that primarily blocks virus attachment to cells, binding at the center of the E protein dimer as part of a new EDE-C epitope class.", "target_protein": "QVELVESGGDVVQPGKSLRLSCAASMHWLRQAPGKGLEWVAVYYADSVKGRFTISRDNSKNTLYLQMNSLTPEDTAVYYCWGQGTLVTVSSGFTFTNYAISSDVNDKAREQAVGTNPWAFDY", "metadata": {"pdb_id": "8jn5", "light_chain_seq": "HIVMTQSPLSLSVTPGQPASISCKSSQISSWGSDGKTYLYWYLQKPGQSPQLLIYEVSSRFSGVSDRFSGSGSGTDFTLKISRVQAEDVGLYYCMQGLHLPLTFGQGTRLEIK", "cdrh1_seq": "GFTFTNYA", "cdrh2_seq": "ISSDVNDK", "cdrh3_seq": "AREQAVGTNPWAFDY", "cdrl1_seq": "QISSWGSDGKTY", "cdrl2_seq": "EVS", "cdrl3_seq": "MQGLHLPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 102]", "cdrh3_split": "val", "cdrh3_cluster": "8jn4", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DENV-290", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Envelope protein, Dengue virus type 3", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "ultrapotent against dengue virus 3 strains, potently neutralize DENV3 with PRNT50 in nanogram/mL range"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 2616, 6914, 16, 14262, 17, 19029, 12, 20733, 1020, 1010, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 11262, 2213, 1927, 13304, 3413, 2601, 23, 18, 1920, 11262, 2213, 1977, 43, 4594, 1927, 1920, 4324, 3146, 5158, 2796, 1988, 4088, 1922, 19230, 5957, 1930, 28104, 1036, 1920, 4423, 3743, 2644, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 5985, 7644, 3413, 8576, 1942, 2094, 16, 2743, 2019, 1920, 4102, 1927, 1920, 47, 2213, 7632, 1966, 3131, 1927, 43, 2814, 3347, 1021, 17, 45, 10095, 2921, 18, 3], "antigen": ["MRCVGVGNRDFVEGLSGATWVDVVLEHGGCVTTMAKNKPTLDIELQKTEATQLATLRKLCIEGKITNITTDSRCPTQGEAVLPEEQDQNYVCKHTYVDRGWGNGCGLFGKGSLVTCAKFQCLEPIEGKVVQYENLKYTVIITVHTGDQHQVGNETQGVTAEITPQASTTEAILPEYGTLGLECSPRTGLDFNEMILLTMKNKAWMVHRQWFFDLPLPWASGATTETPTWNRKELLVTFKNAHAKKQEVVVLGSQEGAMHTALTGATEIQNSGGTSIFAGHLKCRLKMDKLELKGMSYAMCTNTFVLKKEVSETQHGTILIKVEYKGEDAPCKIPFSTEDGQGKAHNGRLITANPVVTKKEEPVNIEAEPPFGESNIVIGIGDNALKINWYKKGSSIGKMFEATARGARRMAILGDTAWDFGSVGGVLNSLGKMVHQIFGSAYTALFSGVSWVMKIGIGVLLTWIGLNSKNTSMSFSCIAIGIITLYLGAVVQA"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human Fab (IGHV1/IGKV1-Kappa) targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (BA.2.12.1 variant). The Spike glycoprotein attaches the virion to the host cell membrane by interacting with host receptors such as ACE2, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. This antibody forms a complex with the Spike glycoprotein. What would the HCDRs be?", "target_protein": "EVQLVQSGAEVKEPGSSVKVSCKASISWVRQAPGQGLEWMGVNYAQKFQGRVTITADESTTTVYMELSSLRSDDTALYYCWGQGTLVTVSSGGSFSTSGIIPIQGTGARDQHIYDSSGHGGLWFDP", "metadata": {"pdb_id": "8cim", "light_chain_seq": "AIRMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKVLIYGASSLHSGVPSRFSGSGSGTDFTLTISRLQPEDFATYYCQQSHSSPRSFGGGTKVEIK", "cdrh1_seq": "GGSFSTSG", "cdrh2_seq": "IIPIQGTG", "cdrh3_seq": "ARDQHIYDSSGHGGLWFDP", "cdrl1_seq": "QSISSY", "cdrl2_seq": "GAS", "cdrl3_seq": "QQSHSSPRS", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8cim", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 6813, 18, 22, 18, 2369, 18, 21, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 2427, 1966, 8298, 1028, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 11424, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["TQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVFRVYSSANNCTFEYVSFKNLREFVFKNIDGYFKIYSKHTPINLPQGFSALEPLVDLPIGINITRFQTLLAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYQYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENLVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A human Fab, T5-1E11 (IGHV4/IGKV2-Kappa), targeting the stabilized Hemagglutinin of Influenza A virus (A/Kiev/1/57). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for membrane fusion during infection. The antibody is designed as a broadly neutralizing antibody targeting the hemagglutinin stem, capable of neutralizing group 1 influenza subtypes. Generate the corresponding HCDRs.", "target_protein": "QVQLQESGPGLVKPSETLSLTCTVSWSWIRQPAGKALEWIGRKSNPSLESRVTMSLDASKDQFSLKLTSVTAADTAVYYCWGQGALVTVSGASVSSYFIYTSGNTAAGRLDYSDTTGYYKPPPLDY", "metadata": {"pdb_id": "8ved", "light_chain_seq": "DVVMTQSPLSLPVTLGQPASISCRSSQGLAFLDGNTYLSWFQQRPGQSPRRLIYKVSNRDSGVPDRFSGSGSRTDFTLKISRVEAEDVGVYYCMQGTHWPLTFGGGTKVEIK", "cdrh1_seq": "GASVSSYF", "cdrh2_seq": "IYTSGNT", "cdrh3_seq": "AAGRLDYSDTTGYYKPPPLDY", "cdrl1_seq": "QGLAFLDGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "MQGTHWPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 115]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "8t1g", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "T5-1E11", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV2", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibody, group 1, influenza"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 24520, 17, 10720, 3242, 12, 20733, 1020, 1006, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 12017, 26141, 1927, 7108, 43, 3413, 12, 43, 19, 8191, 9488, 19, 21, 19, 4786, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 3260, 5289, 2409, 2909, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 26141, 4402, 16, 7131, 1927, 12130, 2210, 21, 7108, 8160, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["DTICIGYHANNSTDTVDTVCEKNVTVTHSVNLLEDSHNGKLCRLKGKAPLQLGNCNIAGWVLGNPECESLLSNRSWSYIAETPNSENGTCFPGDFADYEELREQLSSVSSFERFEIFPKERSWPNHTTRGVTAACPHAMKSSFYKNLVWLTEANGSYPNLSRSYVNNQEKEVLVLWGVHHPSNIEDQRTLYRKDNAYVSVVSSNYNRRFTPEIAKRPKVRGQSGRINYYWTLLEPGDTIIFEATGNLIAPWYAFALSRGPGSGIITSNAPLDECDTKCQTPQGAINSSLPFQNIHPVTIGECPKYVRSTKLRMVTGLRNIPSAIAGFIEGGWTGMMDGWYGYHHQNEQGSGYAADQKSTQNAINCITNKVNSVIEKMNTQFTAVGKEFNKLEKRMENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKNQLRNNAKELGNGCFEFYHKCDNECMESVKNGTYDYPKYSEESKLNREKI"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab (IGHV1/IGKV6-Kappa), one of two antibodies in a neutralizing antibody cocktail (RBD-chAb15 and RBD-chAb45), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (D614G variant). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding or proteolytic cleavage. The antibody is designed as a neutralizing antibody capable of engaging the receptor-binding domain in the context of a multivalent cocktail to neutralize diverse SARS-CoV-2 strains including B.1.1.7.", "target_protein": "EVQLQQSGPELVKPGASVKISCKTSIYWVKQSLGKSLEWIGGTYKQFFKGKATLTVDKSSSTAYMELRSLTSEDSAVYYCWGQGTSVTVSSGYTFTEYTNNPNNDDTARDGYPYYYALDF", "metadata": {"pdb_id": "7eh5", "light_chain_seq": "DIVMTQSQKFMSTSVGDRVSVTCKSSQNVGTNVAWYQQKPGQSPKALIYSASYRYSGVPDHFTGSGSGTDFTLTISNVQSADLAEYFCQQYNNYPWTFGGGTKLEIKRT", "cdrh1_seq": "GYTFTEYT", "cdrh2_seq": "NNPNNDDT", "cdrh3_seq": "ARDGYPYYYALDF", "cdrl1_seq": "QNVGTN", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYNNYPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7w9e", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "cocktail of two nAbs simultaneously bind to all three RBDs, demonstrated potency to neutralize different SARS-CoV-2 pseudovirus strains"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 2340, 1927, 2288, 3788, 1922, 43, 12130, 3533, 12719, 12, 25780, 17, 13297, 5090, 1015, 1930, 25780, 17, 13297, 16290, 1015, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 15304, 3745, 1029, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 2014, 12712, 6404, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 7131, 1927, 15888, 1920, 3148, 17, 2743, 3418, 1922, 1920, 4491, 1927, 43, 5738, 16896, 12719, 1942, 25885, 6445, 20466, 17, 6083, 17, 22, 4046, 2710, 44, 18, 21, 18, 21, 18, 27, 18, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAINPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVVYSSANNCTFEYVSQKNLREFVFKNIDGYFKIYSKHTPIPQGFSALEPLVDLPIGINITRFQTLLAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A murine Fab, 7G7 (IGHV1/IGKV6-Kappa), targeting engineered human Proprotein convertase subtilisin/kexin type 9 (PCSK9). PCSK9 regulates plasma cholesterol homeostasis by binding to low-density lipoprotein receptors and promoting their intracellular degradation. The antibody is designed to inhibit PCSK9 binding to LDLR and preserve cellular LDLR levels, functioning as a cholesterol-lowering antagonist.", "target_protein": "QVQLKQSGAELVRPGASVKLSCKASINWLKKRPGQGLEWIARYYNENFKDKATLTAEKSSSNVYMQLSSLTSEDSAVYFCWGTGTTVTVSSAGYIFTDYYIYPGSGHTARENFYGSSYVDWYFDV", "metadata": {"pdb_id": "6u2f", "light_chain_seq": "DIVMTQSQKFMSTSGGDRVSITCKTSQNVGTAVAWFQQKPGQSPKLLIYSASNRYTGVSDRFTGSGSGTEFIFTISYAQSEDLADYFCHQYSSYPLTFGAGTKLELKRA", "cdrh1_seq": "GYIFTDYY", "cdrh2_seq": "IYPGSGHT", "cdrh3_seq": "ARENFYGSSYVDWYFDV", "cdrl1_seq": "QNVGTA", "cdrl2_seq": "SAS", "cdrl3_seq": "HQYSSYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7bh8", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "7G7", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Proprotein convertase subtilisin/kexin type 9, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "inhibited PCSK9 binding to LDLR and preserved cellular LDLR"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 7135, 6914, 16, 29040, 1027, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 11091, 2616, 12031, 7229, 1921, 14450, 2051, 14745, 1921, 19, 3364, 10960, 2601, 29, 12, 26601, 13, 18, 26601, 7014, 3582, 5463, 7622, 2007, 2743, 1942, 2330, 17, 3824, 9694, 4086, 1930, 7356, 2310, 4776, 4877, 18, 1920, 3533, 1977, 4609, 1942, 2875, 26601, 2743, 1942, 20944, 1930, 15873, 3689, 20944, 2428, 16, 7295, 1966, 43, 5463, 17, 11187, 8151, 18, 3], "antigen": ["TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSREAVTAVAICCRSR"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A human Fab, CAP228-16H (IGHV5/IGLV3-Lambda), targeting the V2 region of the Envelope glycoprotein gp160 of Human immunodeficiency virus 1. The Envelope glycoprotein gp160 attaches the virus to the host lymphoid cell by binding to the primary receptor CD4 and mediates subsequent interactions with chemokine coreceptors. The antibody is designed to mediate ADCC against a broad range of globally prevalent HIV-1 strains through recognition of conserved V2 residues, binding within the Human immunodeficiency virus 1 envelope glycoprotein Gp120.", "target_protein": "EVQLVQSGAEVKKPGESLKISCKGSIGWVRQVPGKGLEWMGIRYRASFQGQVTISADQSSNTAYLQWSSLKASDTAMYYCWGQGTMVTVSSAGYRFPSSWIYPGDGETARHGRGVREVINAFDI", "metadata": {"pdb_id": "6fy0", "light_chain_seq": "YELTQPPSVSVAPGTTATITCGGVDIGSTLVHWYQQRPGQAPLLVIYDDSDRPSGIPERFSGSNSGNMATLTISRVEAGDEADYYCQVWHSTSAVIFGGGTKLTVLSQ", "cdrh1_seq": "GYRFPSSW", "cdrh2_seq": "IYPGDGET", "cdrh3_seq": "ARHGRGVREVINAFDI", "cdrl1_seq": "DIGSTL", "cdrl2_seq": "DDS", "cdrl3_seq": "QVWHSTSAVI", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6fy1", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CAP228-16H", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus 1", "target_domain": "Human immunodeficiency virus 1 envelope glycoprotein Gp120", "functional_role": "other", "evidence_quote": "CAP228 mAbs mediate ADCC against a larger panel of infected cells compared to mAbs from RV144"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 2616, 6914, 16, 2853, 24894, 17, 2641, 1023, 12, 20733, 1020, 1015, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 5133, 1920, 12701, 3031, 1927, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 21, 18, 1920, 11262, 11424, 4882, 16954, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 1930, 10412, 4521, 3719, 1956, 11673, 30435, 3448, 18, 1920, 3533, 1977, 4609, 1942, 8265, 25899, 3316, 43, 4949, 3109, 1927, 13605, 8942, 3525, 17, 21, 4046, 2596, 5708, 1927, 5305, 12701, 4248, 16, 2743, 2651, 1920, 2616, 13141, 3413, 21, 11262, 11424, 16102, 18, 3], "antigen": ["RDKKQKAYALFYRPDVV"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A murine Fab (IGHV1/IGKV3-Kappa) targeting the Hemagglutinin of Influenza A virus (strain A/Vietnam/1203/2004 H5N1). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for penetration of the virus into the cell cytoplasm. This antibody forms a complex with the Hemagglutinin. Please output the HCDRs.", "target_protein": "EVHLQQSGPELVKPGASVKMSCKTSIHWMKQSHGKSLEWIGGTYNQKFKVRATLTVGRSSSTAYMDLRSLTSEDSAVYYCWGAGTTVTVSSAGYTFTEYTIFPNNGDTVRNYGSSYGYFDV", "metadata": {"pdb_id": "8zdw", "light_chain_seq": "DIVLTQSPGSLTVSLGQRATISCRASESVDNFGKSFMHWYQQKPGQSPKLLIYRASNREFGIPARFNGSGSGTDFALTINPVEADDVATYFCQQSNEDPRTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTEYT", "cdrh2_seq": "IFPNNGDT", "cdrh3_seq": "VRNYGSSYGYFDV", "cdrl1_seq": "ESVDNFGKSF", "cdrl2_seq": "RAS", "cdrl3_seq": "QQSNEDPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "8g5b", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus (strain A/Vietnam/1203/2004 H5N1)", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 26141, 1927, 7108, 43, 3413, 12, 3943, 43, 19, 18400, 19, 6103, 1010, 19, 4247, 20128, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 12006, 1927, 1920, 3413, 2460, 1920, 2024, 5239, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 26141, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["DQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A rat Fab (IGHV5/IGKV4-Kappa) targeting the engineered extracellular domain of human Activin receptor type-1 (ALK2). Activin receptor type-1 is a bone morphogenetic protein type I receptor involved in bone, heart, cartilage, nervous, and reproductive system development; it forms heterotetrameric complexes with type II receptors and transduces BMP and activin signaling through SMAD phosphorylation. The antibody, Rm0443, is designed as a neutralizing antibody that inhibits ligand-induced ALK2 signaling by inducing a back-to-back dimer of ALK2 on the cell membrane, thereby preventing heterotopic ossification associated with genetic disorders such as FOP.", "target_protein": "EVQLVESGGGLVQPGRSLKLSCLASMKWIRQAPGKGLEWVASYYADTVKGRFTISRDNARNTLYLQMTSLRSEDTALYYCWGPGTVVTVSSAGSTFSNYGISRSSTYIAAAISTPFYWYFDF", "metadata": {"pdb_id": "7yru", "light_chain_seq": "EIVLTQSPTTMAASPGEKVTLNCLASSSVSYMTWYQQKSGASPKLWIYGTSNLASGVPNRFSGSGSGTSYSLAISSMEAEDVATYYCLHLTSYPPYTFGAGTKLELKRA", "cdrh1_seq": "GSTFSNYG", "cdrh2_seq": "ISRSSTYI", "cdrh3_seq": "AAAISTPFYWYFDF", "cdrl1_seq": "SSVSY", "cdrl2_seq": "GTS", "cdrl3_seq": "LHLTSYPPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7yru", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV4", "is_engineered": true, "target_antigen": "Activin receptor type-1, Homo sapiens", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "Rm0443 inhibited BMP7-induced signaling and prevented ligand-induced heterotopic ossification"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 3067, 6914, 12, 20733, 1020, 1015, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1920, 11091, 5329, 3418, 1927, 2616, 21797, 3148, 2601, 17, 21, 12, 5638, 1028, 13, 18, 21797, 3148, 2601, 17, 21, 1977, 43, 3622, 23359, 2213, 2601, 51, 3148, 3286, 1922, 3622, 16, 4003, 16, 8642, 16, 7580, 16, 1930, 7986, 2433, 2740, 31, 2176, 4952, 19732, 28959, 17118, 5048, 1956, 2601, 2890, 4086, 1930, 30334, 1036, 9809, 1930, 21797, 3197, 2596, 9156, 4050, 18, 1920, 3533, 16, 10625, 14743, 7514, 16, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7042, 5207, 17, 2719, 5638, 1028, 3197, 2007, 7834, 43, 3231, 17, 1942, 17, 3231, 7632, 1927, 5638, 1028, 1990, 1920, 2024, 3260, 16, 6113, 8444, 19732, 27747, 1935, 24189, 2458, 1956, 3299, 4414, 2427, 1966, 5917, 1034, 18, 3], "antigen": ["KLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLP"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A human Fab, Fab40.deltaTrp (IGHV3/IGKV1-Kappa), targeting the engineered Hepatocyte growth factor activator serine protease of Homo sapiens. The serine protease hydrolyzes the inactive zymogen hepatocyte growth factor (HGFsc) to an activated disulfide-linked heterodimer, initiating hepatocyte growth factor receptor signaling. The antibody is designed as an allosteric inhibitor that imposes a conformational change on the substrate binding cleft to prevent catalytic activity, binding within the Peptidase S1 domain.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVGGYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTINGTYIYPAGGATAKWAWPAFDY", "metadata": {"pdb_id": "2wub", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSNRAPATFGQGTKVEIKRT", "cdrh1_seq": "GFTINGTY", "cdrh2_seq": "IYPAGGAT", "cdrh3_seq": "AKWAWPAFDY", "cdrl1_seq": "QDVSTA", "cdrl2_seq": "SAS", "cdrl3_seq": "QQSNRAPAT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 105]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "2wuc", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Fab40.deltaTrp", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Hepatocyte growth factor activator serine protease, Homo sapiens", "target_domain": "Peptidase S1", "functional_role": "other", "evidence_quote": "potent inhibitor of HGFA catalytic activity"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 6914, 4241, 18, 9649, 1997, 1034, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 14675, 2905, 2991, 9518, 8468, 7154, 1927, 16350, 27974, 18, 1920, 8468, 7154, 7222, 20887, 1920, 9078, 15856, 2404, 14675, 2905, 2991, 12, 14757, 12709, 13, 1942, 1925, 4128, 11830, 17, 4624, 15672, 16, 12410, 14675, 2905, 2991, 3148, 3197, 18, 1920, 3533, 1977, 4609, 1966, 1925, 14772, 4106, 1988, 26926, 1036, 43, 8523, 3185, 1990, 1920, 4510, 2743, 14649, 1942, 4625, 6804, 2455, 16, 2743, 2651, 1920, 24050, 4062, 3418, 18, 3], "antigen": ["IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGCRLHKPGVYTRVANYVDWINDRIRP"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A human Fab, 447-52D (IGHV3/IGLV1-Lambda), targeting the V3 loop of Envelope glycoprotein gp160 from Human immunodeficiency virus type 1 subtype B (isolate MN). The V3 loop plays a key role in viral entry into host cells by facilitating attachment to the primary receptor CD4 and subsequent binding to chemokine coreceptors. The antibody is designed as a broadly and potently neutralizing antibody, binding within the V3 domain and preferentially neutralizing clade B viruses that harbor Arg 315 at the V3 crown apex. Generate the corresponding HCDRs.", "target_protein": "EVQLVESGGGLVKPGGSLRLTCVASLNWVRQAPGKGLEWVGRDYAASVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYSCWGKGTTVTVSSAGFTFSDVWIKSRTDGGTTTTDGFIMIRGVSEDYYYYYMDV", "metadata": {"pdb_id": "4m1d", "light_chain_seq": "SVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVLWYQQFPGTAPKLLIYGNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYFCATWDSGLSADWVFGGGTKLTVLSQ", "cdrh1_seq": "GFTFSDVW", "cdrh2_seq": "IKSRTDGGTT", "cdrh3_seq": "TTDGFIMIRGVSEDYYYYYMDV", "cdrl1_seq": "SSNIGNNY", "cdrl2_seq": "GNN", "cdrl3_seq": "ATWDSGLSADWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 119]", "cdrl1_pos": "[24, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 99]", "cdrh3_split": "val", "cdrh3_cluster": "4m1d", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "447-52D", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160 V3 loop, Human immunodeficiency virus type 1 group M subtype B (isolate MN)", "target_domain": "V3", "functional_role": "neutralizing", "evidence_quote": "447\u201352D is one of the most broadly and potently neutralizing anti-V3 mAbs"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 29146, 17, 4764, 1007, 12, 20733, 1020, 1010, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 14307, 5881, 1927, 11262, 11424, 4882, 16954, 2037, 2616, 13141, 3413, 2601, 21, 8856, 44, 12, 9158, 5890, 13, 18, 1920, 14307, 5881, 5705, 43, 3834, 2770, 1922, 4324, 6904, 2460, 4423, 2094, 2007, 12440, 8576, 1942, 1920, 3065, 3148, 4095, 1930, 4521, 2743, 1942, 11673, 30435, 3448, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 1930, 21644, 12130, 3533, 16, 2743, 2651, 1920, 14307, 3418, 1930, 10662, 12130, 11315, 44, 6241, 1988, 14355, 4582, 21413, 2019, 1920, 14307, 18819, 14091, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["CRIHIGPGRAFYTC"]} {"modality_type": "antibody", "text": "Output the HCDRs for an antibody that performs this function: A murine Fab, vFP1.01 (IGHV1/IGKV1-Kappa), targeting the Fusion peptide of HIV-1 Envelope glycoprotein gp160. The Fusion peptide is a critical component of the viral entry machinery that mediates fusion of viral and host cell membranes. The antibody is designed as a neutralizing antibody elicited by immunization with fusion peptide-coupled carriers and prefusion-stabilized envelope trimers, targeting the exposed N-terminal residues of the fusion peptide to achieve cross-clade neutralization of diverse HIV-1 strains.", "target_protein": "QVQLQQSGTELVWPGTSVTLSCKASIHWVKQTPVHGLEWIGAAYNQKFRGKAILTADKSSSTAYMDLRRLTSEDSAVYYCWGTGTTVTVSPAGYTFTDYEIVPKTGYTTRLRNYWYFDV", "metadata": {"pdb_id": "5tkj", "light_chain_seq": "DFLMAQTPLSLPVSLGDQASISCRSSQSIVYSDGNTYLEWYLQRPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLRISRVEAEDLGIYYCFQGSHVPYTFGGGTKLEIKRT", "cdrh1_seq": "GYTFTDYE", "cdrh2_seq": "IVPKTGYT", "cdrh3_seq": "TRLRNYWYFDV", "cdrl1_seq": "QSIVYSDGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQGSHVPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "6cdm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "vFP1.01", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "HIV-1 fusion peptide residue 512-519, Human immunodeficiency virus 1", "target_domain": "Fusion peptide", "functional_role": "neutralizing", "evidence_quote": "vaccine-elicited antibodies capable of neutralizing diverse primary isolates of HIV-1"}}}, "tokenized_instruction": [2, 6647, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 17436, 2052, 2347, 30, 43, 7135, 6914, 16, 15691, 5113, 18, 3287, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 5289, 4207, 1927, 3525, 17, 21, 11262, 11424, 4882, 16954, 18, 1920, 5289, 4207, 1977, 43, 4140, 4594, 1927, 1920, 4324, 6904, 10853, 1988, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 9856, 2007, 10139, 1956, 5289, 4207, 17, 6416, 8974, 1930, 9328, 2670, 17, 12017, 11262, 28220, 16, 5133, 1920, 4616, 56, 17, 4262, 4248, 1927, 1920, 5289, 4207, 1942, 6230, 3567, 17, 11315, 14377, 1927, 6445, 3525, 17, 21, 4046, 18, 3], "antigen": ["AVGIGAVF"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human Fab, ZIKV-195 (IGHV3/IGLV1-Lambda), targeting the E protein of Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013). The E protein is part of the genome polyprotein and mediates viral entry through envelope protein function. The antibody is designed as a neutralizing antibody that engages adjacent E protein protomers on the dimeric virion surface to prevent formation of E protein trimers required for viral-cellular membrane fusion. Please generate the HCDRs for this antibody.", "target_protein": "VQLVESGGGVVHPGRSLRLSCAASMHWVRQAPGKGLEWVAVYYGDSVKGRFTISRDNSKNTLYLQMHSLRAEDTAVYYCWGQGTLVTVSSGFTFSSSAISYDGSNKAKDRDAYNTVGYFAYYYGMDV", "metadata": {"pdb_id": "6mid", "light_chain_seq": "QSVLTQPPSVSEAPRQRVTISCSGSSSNIGNNAVNWYQQLPGKAPKLLIYYDDLLPSGVSDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLTRYVFGTGTKVTVL", "cdrh1_seq": "GFTFSSSA", "cdrh2_seq": "ISYDGSNK", "cdrh3_seq": "AKDRDAYNTVGYFAYYYGMDV", "cdrl1_seq": "SSNIGNNA", "cdrl2_seq": "YDD", "cdrl3_seq": "AAWDDSLTRYV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 115]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 99]", "cdrh3_split": "val", "cdrh3_cluster": "6mid", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ZIKV-195", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "E protein, Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "potently neutralizing human monoclonal antibody ZIKV-195"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 17359, 17, 16030, 12, 20733, 1020, 1010, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 47, 2213, 1927, 28593, 3413, 12, 9158, 17359, 19, 2616, 19, 12941, 15176, 7156, 19, 2813, 8851, 1034, 1038, 19, 3871, 13, 18, 1920, 47, 2213, 1977, 3131, 1927, 1920, 3843, 6240, 5684, 1930, 10412, 4324, 6904, 2596, 11262, 2213, 2347, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 11580, 1036, 6811, 47, 2213, 23583, 27306, 1990, 1920, 18150, 19230, 3154, 1942, 4625, 3337, 1927, 47, 2213, 28220, 3414, 1958, 4324, 17, 3689, 3260, 5289, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTA"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human Fab, Fab668 (IGHV1/IGLV2-Lambda), targeting the junctional peptide region of the Circumsporozoite protein of Plasmodium falciparum. The Circumsporozoite protein is essential for sporozoite development and migration through the vector and vertebrate host, and binds to heparan sulfate proteoglycans on hepatocytes to mediate sporozoite invasion. The antibody is designed to inhibit sporozoite infection by engaging the junctional epitope region, which lies between the N-terminal domain and the NANP repeat region of CSP. Generate the corresponding HCDRs.", "target_protein": "VQLVQSGAEVKKPGASVKVSCKASMHWVRQAPGQRLEWMGWKYSQKFQDRLTITRDTFASTVYMELSSLRSEDTTVYYCWGQGTTVTVSSAGFTFTDYAINAGNGYTARDGFCPSNTCSGYYGMDV", "metadata": {"pdb_id": "6pbv", "light_chain_seq": "SALTQPASVSGSPGQSITISCTGTSSDVGSYNYVSWYQQHPGKAPKLMIYDVNTRPSGVSIRFSASKSGNTASLTVSGLQAEDEAVYYCSSYAGSSTWVFGGGTKLTVLGQ", "cdrh1_seq": "GFTFTDYA", "cdrh2_seq": "INAGNGYT", "cdrh3_seq": "ARDGFCPSNTCSGYYGMDV", "cdrl1_seq": "SSDVGSYNY", "cdrl2_seq": "DVN", "cdrl3_seq": "SSYAGSSTWV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 113]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "6pbv", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Circumsporozoite protein, Plasmodium falciparum", "target_domain": null, "functional_role": "other", "evidence_quote": "antibodies inhibit sporozoite infection in vivo, reducing liver-stage burden"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 6914, 16, 6914, 7283, 1025, 12, 20733, 7390, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 21226, 4207, 3031, 1927, 1920, 28868, 2074, 26553, 2213, 1927, 15663, 13098, 18, 1920, 28868, 2074, 26553, 2213, 1977, 4415, 1958, 9130, 26553, 2740, 1930, 5049, 2596, 1920, 4580, 1930, 13416, 4423, 16, 1930, 6876, 1942, 22024, 8767, 25185, 1990, 9919, 1942, 8265, 9130, 26553, 6254, 18, 1920, 3533, 1977, 4609, 1942, 2875, 9130, 26553, 2909, 2007, 15888, 1920, 21226, 10095, 3031, 16, 2154, 13978, 2192, 1920, 56, 17, 4262, 3418, 1930, 1920, 3529, 1034, 6865, 3031, 1927, 16369, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["GNPDPNANP"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human Fab, S40 (IGHV3/IGKV1-Kappa), targeting the Hemagglutinin of Influenza A virus (A/California/07/2009(H1N1)). Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and internalization, and functions as a class I viral fusion protein responsible for penetration into the cell cytoplasm by mediating membrane fusion. The antibody is designed as a neutralizing antibody discovered from a phage-displayed synthetic antibody library platform targeting the stem epitope region of the HA trimer. Generate the corresponding HCDRs.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVAGYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTIGDFGIWPFGGYTARFVNWDGDYMDY", "metadata": {"pdb_id": "5xhv", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQDVGFYVAWYQQKPGKAPKLLISWSSYLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYYNYPLTFGQGTKVEIKRT", "cdrh1_seq": "GFTIGDFG", "cdrh2_seq": "IWPFGGYT", "cdrh3_seq": "ARFVNWDGDYMDY", "cdrl1_seq": "QDVGFY", "cdrl2_seq": "WSS", "cdrl3_seq": "QQYYNYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5xhv", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S40", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus (A/California/07/2009(H1N1))", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "S40 IgG has weak neutralizing potency against IAV H1N1 CA/09"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 6914, 16, 6934, 1008, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 12, 43, 19, 10191, 19, 6627, 19, 3712, 12, 15355, 13, 13, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 12071, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 12006, 2460, 1920, 2024, 5239, 2007, 10239, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 8117, 2037, 43, 10503, 17, 5822, 6830, 3533, 7337, 6631, 5133, 1920, 4402, 10095, 3031, 1927, 1920, 2118, 20085, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["NLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLR"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human Fab (IGHV1/IGKV3-Kappa) targeting the Spike protein S1 of Severe acute respiratory syndrome coronavirus 2, specifically the BA.2.75 variant. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor to initiate infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. This antibody forms a complex with the Spike protein S1, binding within the Receptor-binding domain (RBD). What would the HCDRs be?", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7yr0", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKR", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike protein S1, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 10429, 2213, 4062, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 16, 4475, 1920, 6813, 18, 22, 18, 4089, 6031, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1942, 11051, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 2213, 4062, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["ITNLCPFHEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGP"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A human Fab (IGHV3/IGKV1-Kappa) targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2, specifically the B.1.617.2 (Delta) variant. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. This antibody forms a complex with the Spike glycoprotein N-terminal domain.", "target_protein": "EVQLVESGGGVVQPGGSLRLSCAASMHWVRQAPGKGLEWVAFYYADSVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCWGQGTLVTVSGFTFNSYGIRYDGGNKANLKDSRYSGSYYDY", "metadata": {"pdb_id": "7soa", "light_chain_seq": "VIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKVDFK", "cdrh1_seq": "GFTFNSYG", "cdrh2_seq": "IRYDGGNK", "cdrh3_seq": "ANLKDSRYSGSYYDY", "cdrl1_seq": "QDIRFY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYDNLPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9c44", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "N-terminal domain (NTD)", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 16, 4475, 1920, 44, 18, 21, 18, 5473, 1027, 18, 22, 12, 9649, 13, 6031, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 11424, 56, 17, 4262, 3418, 18, 3], "antigen": ["QCVNLRQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYKSWMESGVYSSANNCTFEYVSQPFLFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSF"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A human Fab (IGHV1/IGKV3-Kappa) targeting the Thrombin heavy chain of Homo sapiens. Thrombin cleaves bonds after Arg and Lys, converts fibrinogen to fibrin, activates coagulation factors, and functions in blood homeostasis, inflammation, and wound healing. The antibody is designed to bind exosite I with high affinity to modulate thrombin activity while maintaining normal hemostasis, binding within exosite I. Generate the corresponding HCDRs.", "target_protein": "VQLIQSGSAVKKPGASVRVSCKVSIHWVRQAPGKGLEWMGGVYAQQFKGRVTMTEDRSTDTAYMEVNNLRSEDTATYYCWGQGTVVTVASSGYTLTEAALDPQDGETTTGDFSEFEPFSMDYFHF", "metadata": {"pdb_id": "5e8e", "light_chain_seq": "EIVLTQSPATLSLSPGERATLSCRASQNVSSFLAWYQHKPGQAPRLLIYDASSRATDIPIRFSGSGSGTDFTLTISGLEPEDFAVYYCQQRRSWPPLTFGGGTKVEIKRT", "cdrh1_seq": "GYTLTEAA", "cdrh2_seq": "LDPQDGET", "cdrh3_seq": "TTGDFSEFEPFSMDYFHF", "cdrl1_seq": "QNVSSF", "cdrl2_seq": "DAS", "cdrl3_seq": "QQRRSWPPLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "5e8e", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Thrombin heavy chain (Prothrombin), Homo sapiens", "target_domain": "Exosite I", "functional_role": "other", "evidence_quote": "high-affinity, exosite I-directed antibody is consistent with normal hemostasis"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 12388, 7881, 4659, 1927, 16350, 27974, 18, 12388, 23839, 9031, 2256, 4582, 1930, 3629, 16, 21420, 14225, 1942, 9450, 16, 9094, 12441, 2790, 16, 1930, 4088, 1922, 2877, 7622, 16, 4531, 16, 1930, 6376, 7872, 18, 1920, 3533, 1977, 4609, 1942, 4566, 24602, 2394, 51, 1956, 2149, 5173, 1942, 8480, 12388, 2455, 2679, 8231, 2791, 23963, 16, 2743, 2651, 24602, 2394, 51, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human single-chain Fv (scFv), C4 (IGHV3/IGLV2-Lambda), targeting the N-terminal region of Huntingtin. Huntingtin plays a role in microtubule-mediated transport or vesicle function and promotes the formation of autophagic vesicles. The antibody is designed to inhibit mutant huntingtin aggregation by binding the HTT(1-17) region, increasing peptide solubility and sterically hindering the self-association of toxic huntingtin fragments. Please generate the HCDRs for this antibody.", "target_protein": "QVQLQESGGGLVQPGGSLRLSCAASMSWVRQAPGKGLEWVAVYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGRGTLVTVSSGGFTFSSYSISYDGSNKARDRYFDL", "metadata": {"pdb_id": "4rav", "light_chain_seq": "QSALTQPASVSGSPGQSITISCTGTSSDIGAYNYVSWYQQYPGKAPKLLIYDVSNRPSGISNRFSGSKSGDTASLTISGLQAEDEADYYCSSFANSGPLFGGGTKVTVLG", "cdrh1_seq": "GFTFSSYS", "cdrh2_seq": "ISYDGSNK", "cdrh3_seq": "ARDRYFDL", "cdrl1_seq": "SSDIGAYNY", "cdrl2_seq": "DVS", "cdrl3_seq": "SSFANSGPL", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 103]", "cdrl1_pos": "[25, 33]", "cdrl2_pos": "[51, 53]", "cdrl3_pos": "[90, 98]", "cdrh3_split": "val", "cdrh3_cluster": "4rav", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "scFv", "heavy_subclass": "IGHV3", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Huntingtin, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "C4 scFv inhibits mHTT aggregation in vitro and sterically hinders mHTT aggregation"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 2957, 17, 4659, 11417, 12, 19863, 13, 16, 10872, 12, 20733, 1020, 1010, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 56, 17, 4262, 3031, 1927, 16426, 2268, 18, 16426, 2268, 5705, 43, 2770, 1922, 10544, 17, 3434, 4860, 2014, 11502, 2347, 1930, 7383, 1920, 3337, 1927, 15319, 8319, 18, 1920, 3533, 1977, 4609, 1942, 2875, 3606, 16426, 2268, 7883, 2007, 2743, 1920, 5136, 12, 21, 17, 2752, 13, 3031, 16, 3605, 4207, 12506, 1930, 17638, 2169, 15160, 1941, 1920, 3543, 17, 3279, 1927, 6161, 16426, 2268, 6535, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["TLEKLMKAFESLKSF"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab, DH511.11P (IGHV3/IGKV1-Kappa), targeting the membrane-proximal external region (MPER) peptide of HIV-1 gp41. The gp41 MPER is part of the envelope glycoprotein that mediates fusion of viral and host cell membranes during entry. The antibody is designed as a broadly neutralizing antibody targeting the distal MPER epitope, recognizing a transiently exposed intermediate conformation of gp41 that is induced after CD4-mediated Env activation, binding within the MPER domain. Please output the HCDRs.", "target_protein": "QVQLVQSGGGLVKPGGSLTLSCVTSMSWVRQTPGKGLEWVARDYAAPVKGRFIISRDDSRNTLFLHMNNLKTEDTAVYYCWGKGTTVIVSSAGFTFSNTWISRVGDGPIITADEGAPILRFFEWGYYNYYMDV", "metadata": {"pdb_id": "5u3m", "light_chain_seq": "DIRLTQSPSSLSASVGDRITITCRASQSIKDYLNWYKHRPGEAPKLLIYSASKLRSGVSSRFSGSGYGSAFTLTISSLQPEDFATYYCQESYSSVPMYIFGQGTKVDLKRT", "cdrh1_seq": "GFTFSNTW", "cdrh2_seq": "ISRVGDGPII", "cdrh3_seq": "TADEGAPILRFFEWGYYNYYMDV", "cdrl1_seq": "QSIKDY", "cdrl2_seq": "SAS", "cdrl3_seq": "QESYSSVPMYI", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 120]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "5u3m", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DH511.11P", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "gp41 MPER peptide, Human immunodeficiency virus 1", "target_domain": "MPER; binding to GalCer", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing distal MPER bnAbs...neutralized 207 of 208 isolates"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6781, 7912, 1009, 18, 2513, 1034, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 4207, 1927, 3525, 17, 21, 25618, 18, 1920, 25618, 5438, 1915, 1977, 3131, 1927, 1920, 11262, 11424, 1988, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 6583, 5438, 1915, 10095, 16, 15667, 43, 12145, 4616, 6129, 7748, 1927, 25618, 1988, 1977, 2719, 2256, 4095, 17, 3434, 11118, 2936, 16, 2743, 2651, 1920, 5438, 1915, 3418, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["KELDKWASLWNWFDITNWLWYIRKK"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human Fab, NDS.1 (IGHV4/IGKV1-Kappa), targeting the Neuraminidase of Influenza A virus (H3N2v). Neuraminidase catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates to facilitate virus release and spread. The antibody is designed as a neutralizing antibody targeting a conserved epitope on the NA underside (dark side), distinct from the catalytic site, capable of inhibiting viral egress through steric hindrance of NA catalytic activity and conferring protection against diverse H3N2, H3N2v, and H2N2 viruses, binding within the Head of neuraminidase. What would the HCDRs be?", "target_protein": "QVQLRQWGAGLLKPSETLSLTCDVYWTWIRQPPGKGLEWLGETYIPSLKSRVTLSVDTSKGQFSLKLTSVNVADTAVYYCWGQGTPVTVSSGGSFNFYFITHSGSAAGLPIDYDTVHLGYYPMDV", "metadata": {"pdb_id": "8gau", "light_chain_seq": "QMTQSPSSLSASVGDRVTITCRASQGIRNYLAWYQQKPGKVPKLLIYGASTLQSGVPSRFSGSGSGTDFSLTISSLQPEDIATYFCQEYNNAPRTFGQGTKVEIK", "cdrh1_seq": "GGSFNFYF", "cdrh2_seq": "ITHSGSA", "cdrh3_seq": "AGLPIDYDTVHLGYYPMDV", "cdrl1_seq": "QGIRNY", "cdrl2_seq": "GAS", "cdrl3_seq": "QEYNNAPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 113]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "8gau", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "NDS.1", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Neuraminidase, Influenza A virus", "target_domain": "Head of neuraminidase", "functional_role": "neutralizing", "evidence_quote": "inhibited viral egress of nascent particles from infected cells through inhibition of NA catalytic activity"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 6914, 16, 8026, 1036, 18, 21, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 29831, 1927, 7108, 43, 3413, 12, 25234, 1020, 13, 18, 29831, 17097, 1920, 6025, 1927, 4262, 20436, 2687, 4248, 2037, 4324, 1930, 3689, 4235, 30378, 2209, 1942, 6628, 3413, 4012, 1930, 6441, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 43, 5305, 10095, 1990, 1920, 4049, 3302, 2261, 12, 6190, 4159, 13, 16, 4493, 2037, 1920, 6804, 3200, 16, 7131, 1927, 7918, 4324, 15850, 1979, 2596, 17638, 28831, 1927, 4049, 6804, 2455, 1930, 21510, 6202, 3316, 6445, 25234, 16, 25234, 1020, 16, 1930, 4881, 9090, 6241, 16, 2743, 2651, 1920, 4469, 1927, 29831, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["EYRNWSKPQCNITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNGHSNNTVHDRTPYRTLLMNELGVPFHLGTRQVCMAWSSSSCHDGKAWLHVCITGNDNNATASFIYNGRLVDSIGSWSKNILRTQESECVCINGTCTVVMTDGSASGKADTKILFVEEGKIVHISTLSGSAQHVEECSCYPRFPGVRCVCRDNWKGSNRPIVDINVKNYSIVSSYVCSGLVGDTPRKSDSVSSSYCLDPNNEKGGHGVKGWAFDDGNDVWMGRTINETLRLGYETFKVIEGWSKANSKLQTNRQVIVEKGDRSGYSGIFSVEGKSCINRCFYVELIRGRKEETKVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMP"]} {"modality_type": "antibody", "text": "A rat Fab (IGHV5/IGKV3-Kappa) targeting the Interleukin-21 receptor of Homo sapiens. The Interleukin-21 receptor is a receptor for interleukin-21. The antibody is designed to compete with IL-21 for binding to IL-21 R while maintaining favorable biophysical properties and reduced nonspecific interactions, requiring a balance between positive charge necessary for receptor engagement and reduced charge to minimize off-target binding liabilities. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "EVQLVESGGGLVQPGRSLRLSCAASMAWVRQAPKKGLEWVATYYRDSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGVTFSDYHIIYDAARTATWQTTGTPGWFAY", "metadata": {"pdb_id": "7kq7", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCGASQSVSISRFNLMHWYQQKPGHQPKLLIYRASNLASGVPSRFSGSGSGTDFTLTINPLQAEDFATYYCQQSRESPPTFGGGTKVEIKRT", "cdrh1_seq": "GVTFSDYH", "cdrh2_seq": "IIYDAART", "cdrh3_seq": "ATWQTTGTPGWFAY", "cdrl1_seq": "QSVSISRFNL", "cdrl2_seq": "RAS", "cdrl3_seq": "QQSRESPPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "7kq7", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Interleukin-21 receptor, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "antagonizes IL-21 R by competing with IL-21 for overlapping binding determinants"}}}, "tokenized_instruction": [2, 43, 3067, 6914, 12, 20733, 1020, 1015, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 9198, 17, 2900, 3148, 1927, 16350, 27974, 18, 1920, 9198, 17, 2900, 3148, 1977, 43, 3148, 1958, 9198, 17, 2900, 18, 1920, 3533, 1977, 4609, 1942, 17269, 1956, 2614, 17, 2900, 1958, 2743, 1942, 2614, 17, 2900, 60, 2679, 8231, 9327, 17470, 3879, 1930, 3028, 12720, 3719, 16, 8887, 43, 6766, 2192, 2843, 7051, 4680, 1958, 3148, 9577, 1930, 3028, 7051, 1942, 9491, 4013, 17, 2758, 2743, 25700, 12039, 2569, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["CPDLVCYTDYLQTVICILEMWNLHPSTLTLTWQDQYEELKDEATSCSLHRSAHNATHATYTCHMDVFHFMADDIFSVNITDQSGNYSQECGSFLLAESIKPAPPFNVTVTFSGQYNISWRSDYEDPAFYMLKGKLQYELQYRNRGDPWAVSPRRKLISVDSRSVSLLPLEFRKDSSYELQVRAGPMPGSSYQGTWSEWSDPVIFQTQS"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A murine Fab, 2C11 (IGHV1/IGKV12-Kappa), targeting an engineered isoform 2 of Protein-serine O-palmitoleoyltransferase porcupine from Homo sapiens. Porcupine is a key regulator of the Wnt signaling pathway that mediates the attachment of palmitoleate to Wnt proteins, a modification required for efficient binding to frizzled receptors. The antibody is designed as a structural tool to stabilize native PORCN for cryo-electron microscopy studies of substrate-bound and inhibitor-bound states, enabling visualization of the catalytic mechanism of Wnt acylation.", "target_protein": "EIQLQQSGAELVKPGASVKMSCKVSMNWVKQSHGKSLEWIGNNYNQKFTGKATFTVDRSSSTAYMQLDSLTSEDSAVYYCWGQGTLVTVSSGYSFTGYNINPYYVSTARSYGSSHTFAY", "metadata": {"pdb_id": "7ura", "light_chain_seq": "DIHMTQSPASLSAFVGETVTITCRTSENIFSYLAWYQQKQGKSPQLLVYNAKTLTSGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGSPYTFGGGTKLEIK", "cdrh1_seq": "GYSFTGYN", "cdrh2_seq": "INPYYVST", "cdrh3_seq": "ARSYGSSHTFAY", "cdrl1_seq": "ENIFSY", "cdrl2_seq": "NAK", "cdrl3_seq": "QHHYGSPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7ura", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2C11", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV12", "is_engineered": true, "target_antigen": "Protein-serine O-palmitoleoyltransferase porcupine (isoform 2), Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "monoclonal antibody denoted 2C11 that explicitly binds to native PORCN...to capture the substrate-bound state"}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 6921, 3242, 12, 20733, 7390, 19, 7021, 1040, 7390, 1028, 17, 12093, 13, 16, 5133, 1925, 11091, 6174, 22, 1927, 2213, 17, 8468, 57, 17, 13615, 2456, 10921, 9961, 4572, 18021, 12184, 2037, 16350, 27974, 18, 4572, 18021, 12184, 1977, 43, 3834, 7888, 1927, 1920, 7028, 3197, 3374, 1988, 10412, 1920, 8576, 1927, 13615, 2456, 2010, 1942, 7028, 2697, 16, 43, 6295, 3414, 1958, 5807, 2743, 1942, 9081, 18559, 2824, 4086, 18, 1920, 3533, 1977, 4609, 1966, 43, 4346, 5229, 1942, 13448, 6196, 4572, 7814, 1958, 15822, 17, 4995, 5441, 2351, 1927, 4510, 17, 4124, 1930, 4106, 17, 4124, 4376, 16, 12180, 9966, 1927, 1920, 6804, 2856, 1927, 7028, 11337, 1943, 18, 3], "antigen": ["FSRQEFFQQLLQGCLLPTAQQGLDQIWLLLAICLACRLLWRLGLPSYLKHASTVAGGFFSLYHFFQLHMVWVVLLSLLCYLVLFLCRHSSHRGVFLSVTILIYLLMGEMHMVDTVTWHKMRGAQMIVAMKAVSLGFDLDRGEVGTVPSPVEFMGYLYFVGTIVFGPWISFHSYLQAVQGRPLSCRWLQKVARSLALALLCLVLSTCVGPYLFPYFIPLNARWLRAYESAVSFHFSNYFVGFLSEATATLAGAGFTEEKDHLEWDLTVSKPLNVELPRSMVEVVTSWNLPMSYWLNNYVFKNALRLGTFSAVLVTYAASALLHGFSFHLAAVLLSLAFITYVEHVLRKRLARILSACVLSKRCPPDCSHQHRLGLGVRALNLLFGALAIFHLAYLGSLFDVYGMAYTVHKWSELSWASHWVTFGCWIFYRLIG"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human Fab (IGHV3/IGLV6-Lambda) targeting the engineered Transmembrane protease serine 2 (TMPRSS2) catalytic chain of Homo sapiens. TMPRSS2 is a plasma membrane-anchored serine protease that facilitates human coronavirus infections via proteolytic cleavage of ACE2 receptor and activation of coronavirus spike glycoproteins, and is essential for spread and pathogenesis of influenza A virus. The antibody is designed to inhibit TMPRSS2 enzymatic activity and block the interaction between TMPRSS2 and viral receptor-binding domains, providing dual antiviral protection against multiple coronavirus and influenza strains, binding within the Peptidase S1 domain. What would the HCDRs be?", "target_protein": "QVQLQESGGDLVQPGGSLRLSCAASMTWVRQAPGKGLEWVSDNYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTFSSSAISRNGGSTAREGYDFWSGRERRYYYYGMDV", "metadata": {"pdb_id": "9jd1", "light_chain_seq": "NFMLTQPHSMSESPGKTVTISCTRSSGSIASNYVQWYQQRPGSSPTTVIYDDNQRPSGVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSNVIFGGGTKLTVLRT", "cdrh1_seq": "GFTFSSSA", "cdrh2_seq": "ISRNGGST", "cdrh3_seq": "AREGYDFWSGRERRYYYYGMDV", "cdrl1_seq": "SGSIASNY", "cdrl2_seq": "DDN", "cdrl3_seq": "QSYDSSNVI", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 117]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[91, 99]", "cdrh3_split": "val", "cdrh3_cluster": "9jd1", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV6", "is_engineered": true, "target_antigen": "Transmembrane protease serine 2, Homo sapiens", "target_domain": "Peptidase S1", "functional_role": "other", "evidence_quote": "antibodies targeting TMPRSS2 potently inhibit TMPRSS2 activity and block viral entry"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 28961, 25606, 17, 18279, 13, 5133, 1920, 11091, 9117, 7154, 8468, 22, 12, 23992, 5675, 13262, 13, 6804, 4659, 1927, 16350, 27974, 18, 23992, 5675, 13262, 1977, 43, 3582, 3260, 17, 17199, 8468, 7154, 1988, 11374, 2616, 5548, 10703, 5024, 3454, 12712, 6404, 1927, 8298, 1028, 3148, 1930, 2936, 1927, 5548, 10703, 10429, 16268, 16, 1930, 1977, 4415, 1958, 6441, 1930, 6559, 1927, 7108, 43, 3413, 18, 1920, 3533, 1977, 4609, 1942, 2875, 23992, 5675, 13262, 8145, 2455, 1930, 3367, 1920, 2835, 2192, 23992, 5675, 13262, 1930, 4324, 3148, 17, 2743, 4682, 16, 5453, 7064, 10129, 6202, 3316, 3137, 5548, 10703, 1930, 7108, 4046, 16, 2743, 2651, 1920, 24050, 4062, 3418, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["IVGGESALPGAWPWQVSLHVQNVHVCGGSIITPEWIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVDSCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRADGEF"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab (IGHV1/IGKV1-Kappa), antibody 0722, targeting the Spike glycoprotein of Middle East respiratory syndrome-related coronavirus. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host DPP4 receptor and mediates fusion of viral and cellular membranes through conformational transitions between pre-fusion, pre-hairpin intermediate, and post-fusion states. This antibody forms a complex with the Spike glycoprotein ectodomain trimer.", "target_protein": "QVQLVQSGAEVKKPGSSVKVSCKASISWVRQAPGQGLEWMGGNYAQQFQGRVTITADESTTTAYMELSRLTSEDTAVYYCWGQGTLVTVSSAGGTFSIYAIIPIFGTAARQMTAYDYWNPSFDY", "metadata": {"pdb_id": "7v5j", "light_chain_seq": "DIVMTQTPSSLSASVGDRVTITCRASEDITSYLNWYQLKPGKAPMFLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPTFGGGTKVEIKRT", "cdrh1_seq": "GGTFSIYA", "cdrh2_seq": "IIPIFGTA", "cdrh3_seq": "ARQMTAYDYWNPSFDY", "cdrl1_seq": "EDITSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSYSTPPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7v5j", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Spike glycoprotein, Middle East respiratory syndrome-related coronavirus", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 3533, 6627, 4460, 16, 5133, 1920, 10429, 11424, 1927, 5576, 10319, 5481, 4741, 17, 2712, 5548, 10703, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 16423, 1006, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 10673, 2192, 2097, 17, 5289, 16, 2097, 17, 14565, 6129, 16, 1930, 2753, 17, 5289, 4376, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 11424, 27385, 20085, 18, 3], "antigen": ["YVDVGPDSVKSACIEVDIQQTFFDKTWPRPIDVSKADGIIYPQGRTYSNITITYQGLFPYQGDHGDMYVYSAGHATGTTPQKLFVANYSQDVKQFANGFVVRIGAAANSTGTVIISPSTSATIRKIYPAFMLGSSVGNFSDGKMGRFFNHTLVLLPDGCGTLLRAFYCILEPRSGNHCPAGNSYTSFATYHTPATDCSDGNYNRNASLNSFKEYFNLRNCTFMYTYNITEDEILEWFGITQTAQGVHLFSSRYVDLYGGNMFQFATLPVYDTIKYYSIIPHSIRSIQSDRKAWAAFYVYKLQPLTFLLDFSVDGYIRRAIDCGFNDLSQLHCSYESFDVESGVYSVSSFEAKPSGSVVECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKLKIASQLGNCVEYSLYGVSGRGVFQNCTAVGVRQQRFVYDAYQNLVGYYSDDGNYYCLRACVSVPVSVIYDKETKTHATLFGSVACEHISSTMSQYSRSTRSMLKPVGCVLGLVNSSLFVEDCKLPLGQSLCALPDTPSTMRLASIAFNHPIQVDQLNSSYFKLSIPTNFSFGVTQEYIQTTIQKVTVDCKQYVCNGFQKCEQLLREYGQFCSKINQALHGANLRQDDSVRNLFASVKSSQSSPIIPGFGGDFNLTLLEPVARSAIEDLLFDKVTIADPGYMQGYDDCMQQICAQYVAGYKVLPPLMDVNMEAAYTSSLLGSIAGVGWTAGLSSFAAIPFAQSIFYRLNGVGITQQVLSENQKLIANKFNQALGAMQTGFTTTNEAFQKVQDAVNNNAQALSKLASELSNTFGAISASIGDIIQRLDVLEQDAQIDRLINGRLTTLNAFVAQQLVRSESAALSAQLAKDKVNECVKAQSKRSGFCGQGTHIVSFVVNAPNGLYFMHVGYYPSNHIEVVSAYGLCDAANPTNCIAPVNGYFIKIVDEWSYTGSSFYAPEPITSLNTKYVA"]} {"modality_type": "antibody", "text": "A human Fab, 4E10 (IGHV1/IGKV3-Kappa), targeting the Envelope glycoprotein gp160 of Human immunodeficiency virus 1, specifically the MPER region. The Envelope glycoprotein gp160 is proteolytically cleaved to produce gp120 and gp41, which attach the virus to the host lymphoid cell by binding to the primary receptor CD4 and chemokine coreceptors. The antibody is designed as a neutralizing antibody that engages a composite epitope comprising both the MPER peptide and viral membrane lipids, particularly phosphatidic acid and phosphatidylglycerol, requiring coordinated binding to both protein and lipid components of the viral surface. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "QVQLVQSGAEVKRPGSSVTVSCKASLSWVRQAPGRGLEWMGGNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCWGQGTLVTVSSAGGSFSTYAVIPLLTITAREGTTLGKPIGAFAH", "metadata": {"pdb_id": "4xcf", "light_chain_seq": "EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRT", "cdrh1_seq": "GGSFSTYA", "cdrh2_seq": "VIPLLTIT", "cdrh3_seq": "AREGTTLGKPIGAFAH", "cdrl1_seq": "QSVGNNK", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYGQSLST", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "5x08", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "4E10", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160 (gp41), Human immunodeficiency virus 1", "target_domain": "MPER", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody responses against the highly conserved MPER region"}}}, "tokenized_instruction": [2, 43, 2616, 6914, 16, 10800, 2930, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 21, 16, 4475, 1920, 5438, 1915, 3031, 18, 1920, 11262, 11424, 4882, 16954, 1977, 12712, 2169, 10246, 1942, 5074, 16102, 1930, 25618, 16, 2154, 5823, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 1930, 11673, 30435, 3448, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 11580, 1036, 43, 7895, 10095, 10351, 2321, 1920, 5438, 1915, 4207, 1930, 4324, 3260, 8238, 16, 4443, 2766, 8525, 1935, 2687, 1930, 10951, 18207, 16, 8887, 11651, 2743, 1942, 2321, 2213, 1930, 4486, 4178, 1927, 1920, 4324, 3154, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["NWWDITNWLWYIKKKK"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A murine Fab, 8D3 (IGHV1/IGKV6-Kappa), targeting the Receptor-binding domain (RBD) of the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (Delta variant). The Spike glycoprotein attaches the virion to the host cell membrane by interacting with the ACE2 receptor to initiate infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a broadly neutralizing antibody capable of cross-neutralizing multiple SARS-CoV-2 variants including Delta, Beta, and Kappa with potency comparable to wild-type strain neutralization.", "target_protein": "EVQLQQSGPELVKPGASVKISCKTSMYWVKQSHGKSLEWIGGSYNQNFKGKATLTVDRSSSTAYMELRSLTSEDSAVYYCWGQGTSVTVSSAGYTFTEYTINPNIGDTARDGYPYYYALDH", "metadata": {"pdb_id": "7w9f", "light_chain_seq": "DIVMTQSQKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALIYSTSYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQYNSYPYTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTEYT", "cdrh2_seq": "INPNIGDT", "cdrh3_seq": "ARDGYPYYYALDH", "cdrl1_seq": "QNVGTN", "cdrl2_seq": "STS", "cdrl3_seq": "QQYNSYPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7w9e", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "8D3", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "potent cross-neutralization with IC50s against Delta, Beta, and Kappa comparable to those against WT"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 7135, 6914, 16, 23865, 1010, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 1927, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 9649, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 1920, 8298, 1028, 3148, 1942, 11051, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 7131, 1927, 3567, 17, 12130, 3137, 20466, 17, 6083, 17, 22, 4936, 2710, 9649, 16, 4666, 16, 1930, 12093, 1956, 10397, 5596, 1942, 3576, 17, 2601, 3943, 14377, 18, 3], "antigen": ["TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A human Fab, BD-508 (IGHV3/IGKV1-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors, initiating infection and mediating fusion of viral and cellular membranes. The antibody is designed as a neutralizing antibody targeting the Receptor-binding domain (RBD), with sensitivity to RBD mutations including K417N, E484K, and N501Y found in circulating variants.", "target_protein": "VQLVESGGGLVQPGGSLRLSCAASMTWVRQAPGKGLEWVSVFYADSVKGRFTISRHNSKNTLFLQMNSLRAEDTAVYYCWGQGTTVTVSSAGFIVSSNYIYSGGSTARDAQNYGMDV", "metadata": {"pdb_id": "7e86", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIFAASSLQTGAPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPYTFGQGTKLEIKRT", "cdrh1_seq": "GFIVSSNY", "cdrh2_seq": "IYSGGST", "cdrh3_seq": "ARDAQNYGMDV", "cdrl1_seq": "QSISSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSYSTPPYT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 55]", "cdrh3_pos": "[94, 104]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "7e86", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "BD-508", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "BD-508 is a class 1 NAb that neutralizes SARS-CoV-2"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 2616, 6914, 16, 5238, 17, 2761, 1025, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 16, 12410, 2909, 1930, 10239, 5289, 1927, 4324, 1930, 3689, 5726, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 1956, 3802, 1942, 25780, 3527, 2710, 26641, 3952, 1022, 16, 18157, 11068, 1040, 16, 1930, 56, 3382, 1009, 1012, 2435, 1922, 7396, 4936, 18, 3], "antigen": ["NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGH"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human Fab, PGZL1 (IGHV1/IGKV3-Kappa), targeting the membrane-proximal external region (MPER) of the Envelope glycoprotein gp41 of Human immunodeficiency virus 1. The gp41 MPER is a conserved epitope on the viral membrane that mediates fusion of viral and host cell membranes during entry. The antibody is designed as a broadly neutralizing antibody with a 15-residue CDRH3 and reduced polyreactivity, engaging the MPER in its membrane-embedded context on the viral surface. Can you generate its HCDRs?", "target_protein": "EVQLVQSGGEVKRPGSSVTVSCKATFNWVRQAPGQGPEWMGGNYGQKFQGRLTIRADKSTTTVFLDLSGLTSADTATYYCWGQGTVITVSSAGGTFSTLAIVPLFSIVAREGEGWFGKPLRAFEF", "metadata": {"pdb_id": "6o3j", "light_chain_seq": "VVMTQSPGTLSLSPGERATLSCRASQSVSGGALAWYQQKPGQAPRLLIYDTSSRPTGVPGRFSGSGSGTDFSLTISRLEPEDFAVYYCQQYGTSQSTFGQGTRLEIKRT", "cdrh1_seq": "GGTFSTLA", "cdrh2_seq": "IVPLFSIV", "cdrh3_seq": "AREGEGWFGKPLRAFEF", "cdrl1_seq": "QSVSGGA", "cdrl2_seq": "DTS", "cdrl3_seq": "QQYGTSQST", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[25, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6mto", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "PGZL1", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp41, Human immunodeficiency virus 1", "target_domain": "MPER; binding to GalCer", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibody from an HIV-infected person that recognizes the membrane-proximal external region (MPER)"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 6914, 16, 5306, 26262, 1009, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 1927, 1920, 11262, 11424, 25618, 1927, 2616, 13141, 3413, 21, 18, 1920, 25618, 5438, 1915, 1977, 43, 5305, 10095, 1990, 1920, 4324, 3260, 1988, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1956, 43, 2461, 17, 6181, 20170, 18649, 1930, 3028, 4286, 1936, 5454, 16, 15888, 1920, 5438, 1915, 1922, 2496, 3260, 17, 8222, 4491, 1990, 1920, 4324, 3154, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["NWFDITNWLWYIKKK"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A murine Fab, F26G19 (IGHV1/IGKV9-Kappa), targeting the Spike glycoprotein of SARS coronavirus. The Spike glycoprotein attaches the virion to the cell membrane by interacting with the host ACE2 receptor, initiating infection. The antibody is designed as a neutralizing antibody that blocks receptor binding by competing with ACE2 for engagement of the receptor-binding domain (RBD).", "target_protein": "EVQLEESGTVLARPGASVKMSCKASMHWIKQRPGQGLEWIGATYNQKFKDKAKLTAVTSTSSAYMELSSLTNEDSAVYFCWGQGTSVTVSSAGYTFTTYRIYPGNSDTTREGIPQLLRTLDY", "metadata": {"pdb_id": "3bgf", "light_chain_seq": "DILMTQSPSSLSASLGERVSLTCRASQEISGYLSWLQEKPDGTIKRLIYAASTLDSGVPKRFSGSRSGSDYSLTISSLESEDFADYYCLQYVSYPWTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTTYR", "cdrh2_seq": "IYPGNSDT", "cdrh3_seq": "TREGIPQLLRTLDY", "cdrl1_seq": "QEISGY", "cdrl2_seq": "AAS", "cdrl3_seq": "LQYVSYPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3bgf", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "F26G19", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV9", "is_engineered": false, "target_antigen": "Spike glycoprotein, SARS coronavirus", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "F26G19 likely neutralizes SARS-CoV by blocking the virus\u2013host cell interaction"}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 11063, 1016, 9114, 1026, 12, 20733, 7390, 19, 7021, 1040, 1020, 1026, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 20466, 5548, 10703, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 1920, 4423, 8298, 1028, 3148, 16, 12410, 2909, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 3148, 2743, 2007, 11743, 1956, 8298, 1028, 1958, 9577, 1927, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 3], "antigen": ["CPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSF"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human Fab, hH35 (IGHV7/IGLV7-Lambda), targeting the Serine protease hepsin. Hepsin is a type II transmembrane serine protease that cleaves extracellular substrates and contributes to proteolytic processing of growth factors such as HGF and MST1/HGFL, and plays a role in cell growth and maintenance of cell morphology. The antibody is designed to inhibit hepsin enzymatic activity through an allosteric mechanism, binding distal from the active site. Generate the corresponding HCDRs.", "target_protein": "QVQLVQSGSELKKPGASVKVSCKASMRWVRQAPGQGLEWMGWTYADDFKGRFVFSLDTSVSTAYLQISSLKAEDTAVYYCWGQGTLVTVSSAGYTFTDYSINTETGSPARGFAY", "metadata": {"pdb_id": "3t2n", "light_chain_seq": "QTVVTQEPSLTVSPGGTVTLTCRSSTGAVTTSNYANWVQQKPGQAFRGLIGDTNNRAPWTPARFSGSLLGGKAALTLSGVQPEDEAEYYCALWYSNHFIFGSGTKVTVLGQ", "cdrh1_seq": "GYTFTDYS", "cdrh2_seq": "INTETGSP", "cdrh3_seq": "ARGFAY", "cdrl1_seq": "TGAVTTSNY", "cdrl2_seq": "DTN", "cdrl3_seq": "ALWYSNHFI", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 101]", "cdrl1_pos": "[25, 33]", "cdrl2_pos": "[51, 53]", "cdrl3_pos": "[90, 98]", "cdrh3_split": "val", "cdrh3_cluster": "3t2n", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "hH35", "antibody_format": "Fab", "heavy_subclass": "IGHV7", "light_subclass": "IGLV7", "is_engineered": false, "target_antigen": "Serine protease hepsin, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "antibody that selectively inhibits human hepsin enzymatic activity"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 6914, 16, 9645, 5798, 12, 20733, 1020, 1027, 19, 28961, 1020, 1027, 17, 18279, 13, 16, 5133, 1920, 8468, 7154, 3357, 6777, 18, 3357, 6777, 1977, 43, 2601, 2890, 9117, 8468, 7154, 1988, 23839, 5329, 6249, 1930, 7624, 1942, 12712, 4587, 1927, 2905, 2790, 2427, 1966, 14757, 1930, 16195, 1009, 19, 14757, 1024, 16, 1930, 5705, 43, 2770, 1922, 2024, 2905, 1930, 6291, 1927, 2024, 6076, 18, 1920, 3533, 1977, 4609, 1942, 2875, 3357, 6777, 8145, 2455, 2596, 1925, 14772, 2856, 16, 2743, 6583, 2037, 1920, 3500, 3200, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["QEPLYPVQVSSADARLMVFDKTEGTWRLLCSSRSNARVAGLSCEEMGFLRALTHSELDVRTAGANGTSGFFCVDEGRLPHTQRLLEVISVCDCPRGRFLAAICQDCGRRKLPRDTSLGRWPWQVSLRYDGAHLCGGSLLSGDWVLTAAHCFPERNRVLSRWRVFAGAVAQASPHGLQLGVQAVVYHGGYLPFRDPNSEENSNDIALVHLSSPLPLTEYIQPVCLPAAGQALVDGKICTVTGWGVLQEARVPIISNDVCNGADFYGNQIKPKMFCAGYPGDSGGPFVCEDSISRTPRWRLCGIVSLAQKPGVYTKVSDFREWIFQAIKTHSEASGMVTQL"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab (IGHV1/IGKV3-Kappa) targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2, one of three antibodies in a triple-antibody complex (BD604, S309, and S304). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes during entry. The antibody is designed as a neutralizing antibody, binding within the Receptor-binding domain (RBD) to neutralize Omicron sub-variants.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7x1m", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "neutralizing mAbs against Omicron sub-variants BA.1, BA.1.1, BA.2, and BA.3"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 16, 2340, 1927, 2559, 3788, 1922, 43, 10073, 17, 3533, 2796, 12, 5238, 5127, 1006, 16, 6080, 13192, 16, 1930, 6080, 14743, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 1942, 25885, 7254, 1935, 2830, 2316, 17, 4936, 18, 3], "antigen": ["TNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGP"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A murine Fab, A6 (IGHV8/IGKV13-Kappa), targeting the Interferon gamma receptor 1 of Homo sapiens. Interferon gamma receptor 1 is a receptor subunit for interferon gamma that plays crucial roles in antimicrobial, antiviral, and antitumor responses by activating effector immune cells and enhancing antigen presentation. The antibody is designed as a neutralizing antibody targeting the N-terminal immunoglobulin-like domain, specifically the loop connecting beta-strands C and C'.", "target_protein": "AVKLQESGPGILKPSQTLSLTCSFSVGWIRQSSGKGLEWLAHYYNPSLKSRLTISKDTSRNQVFLKITSVATADTATYYCWGQGTTVTVSSAGFSLTTYGMGIWWDDDKARRAPFYGNHAMDY", "metadata": {"pdb_id": "1jrh", "light_chain_seq": "SVEMTQSPSSFSVSLGDRVTITCKASEDIYNRLAWYQQKPGNAPRLLISGATSLETEVPSRFSGSGSGKDYTLSITSLQTEDVATYYCQQYWSTWTFGGGTKLEIKRA", "cdrh1_seq": "GFSLTTYGMG", "cdrh2_seq": "IWWDDDK", "cdrh3_seq": "ARRAPFYGNHAMDY", "cdrl1_seq": "EDIYNR", "cdrl2_seq": "GAT", "cdrl3_seq": "QQYWSTWT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "1jrh", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "A6", "antibody_format": "Fab", "heavy_subclass": "IGHV8", "light_subclass": "IGKV13", "is_engineered": false, "target_antigen": "Interferon gamma receptor 1, Homo sapiens", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibodies...mapped by homolog scanning mutagenesis"}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 24759, 12, 20733, 1020, 1025, 19, 7021, 1040, 7390, 1010, 17, 12093, 13, 16, 5133, 1920, 10001, 7034, 3148, 21, 1927, 16350, 27974, 18, 10001, 7034, 3148, 21, 1977, 43, 3148, 5903, 1958, 10001, 7034, 1988, 5705, 6608, 5456, 1922, 8003, 16, 10129, 16, 1930, 11775, 3387, 2007, 8019, 7917, 3743, 2094, 1930, 9221, 4730, 6544, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 56, 17, 4262, 11837, 17, 3189, 3418, 16, 4475, 1920, 5881, 15031, 4666, 17, 13214, 45, 1930, 45, 11, 18, 3], "antigen": ["SVPTPTNVTIESYNMNPIVYWEYQIMPQVPVFTVEVKNYGVKNSEWIDACINISHHYCNISDHVGDPSNSLWVRVKARVGQKESAYAKSEEFAVS"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A murine Fab, PT3 (IGHV5/IGKV14-Kappa), targeting a phosphorylated tau peptide (phosphorylated at threonine 212 and threonine 217) derived from human Microtubule-associated protein tau. Tau promotes microtubule assembly and stability and functions as a linker protein between axonal microtubules and neural plasma membrane components. The antibody is designed to neutralize tau seeding and deplete tau seeds as a disease-modifying strategy for Alzheimer's disease.", "target_protein": "GGDLVKPGGSLKLSCAASMSWVRQNPEKRLEWVASYYPNSVKGRFTISRDNARNILYLQMSSLRSEDTALYYCWGQVTLVTVSAAGFTFSSYAISKGGNTARGWGDYGWFAY", "metadata": {"pdb_id": "6xli", "light_chain_seq": "DIKMTQSPSSMYASLGERVTITCKASQDINRYLNWFQQKPGKSPKTLIYRANRLLDGVPSRFSGSGSGQDYSLTISSLDYEDMGIYYCLQYDEFPLTFGDGTKLELKRT", "cdrh1_seq": "GFTFSSYA", "cdrh2_seq": "ISKGGNT", "cdrh3_seq": "ARGWGDYGWFAY", "cdrl1_seq": "QDINRY", "cdrl2_seq": "RAN", "cdrl3_seq": "LQYDEFPLT", "cdrh1_pos": "[18, 25]", "cdrh2_pos": "[43, 49]", "cdrh3_pos": "[88, 99]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6xli", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "PT3", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV14", "is_engineered": false, "target_antigen": "Tau Phosphopeptide (phosphorylated at T212/T217), Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "neutralization of tau seeding by immunodepletion assays"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 7135, 6914, 16, 4401, 1010, 12, 20733, 1020, 1015, 19, 7021, 1040, 7390, 1006, 17, 12093, 13, 16, 5133, 43, 7199, 7462, 4207, 12, 7199, 2019, 13143, 17251, 1930, 13143, 18209, 13, 3595, 2037, 2616, 10544, 17, 2458, 2213, 7462, 18, 7462, 7383, 10544, 5957, 1930, 5057, 1930, 4088, 1966, 43, 11040, 2213, 2192, 10623, 12444, 1930, 5181, 3582, 3260, 4178, 18, 1920, 3533, 1977, 4609, 1942, 25885, 7462, 16777, 1930, 27287, 7462, 9869, 1966, 43, 2573, 17, 12691, 4884, 1958, 9116, 11, 61, 2573, 18, 3], "antigen": ["SRPSLPPPTRE"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab, sarilumab (IGHV3/IGKV1-Kappa), targeting the Interleukin-6 receptor subunit alpha. IL-6R is part of the receptor for interleukin-6 and mediates classic and trans-signaling pathways that regulate immune response, acute-phase reactions, and hematopoiesis. The antibody is designed to inhibit IL-6 signaling by blocking the IL-6 binding site on IL-6R, thereby preventing IL-6/IL-6R/gp130 complex formation and downstream signal transduction.", "target_protein": "VQLVESGGGLVQPGRSLRLSCAASMHWVRQAPGKGLEWVSGGYADSVKGRFTISRDNAENSLFLQMNGLRAEDTALYYCWGQGTMVTVSSARFTFDDYAISWNSGRIAKGRDSFDI", "metadata": {"pdb_id": "8iow", "light_chain_seq": "DIQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLIYGASSLESGVPSRFSGSGSGTDFTLTISSLQPEDFASYYCQQANSFPYTFGQGTKLEIKRT", "cdrh1_seq": "RFTFDDYA", "cdrh2_seq": "ISWNSGRI", "cdrh3_seq": "AKGRDSFDI", "cdrl1_seq": "QGISSW", "cdrl2_seq": "GAS", "cdrl3_seq": "QQANSFPYT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 103]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8iow", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "sarilumab", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Interleukin-6 receptor subunit alpha, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "inhibit IL-6/IL-6R signaling by competing for the IL-6 binding site"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 16, 9851, 1970, 6683, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 9198, 17, 26, 3148, 5903, 4595, 18, 2614, 17, 29680, 1977, 3131, 1927, 1920, 3148, 1958, 9198, 17, 26, 1930, 10412, 12211, 1930, 2127, 17, 3197, 3873, 1988, 5741, 3743, 2644, 16, 3939, 17, 3193, 5298, 16, 1930, 21941, 18, 1920, 3533, 1977, 4609, 1942, 2875, 2614, 17, 26, 3197, 2007, 7472, 1920, 2614, 17, 26, 2743, 3200, 1990, 2614, 17, 29680, 16, 6113, 8444, 2614, 17, 26, 19, 2614, 17, 29680, 19, 4882, 12285, 2796, 3337, 1930, 5863, 2733, 8201, 18, 3], "antigen": ["QGCGILQPDPPANITVTAVARNPRWLSVTWQDPHSWNSSFYRLRFELRYRAERSKTFTTWMVKDLQHHCVIHDAWSGLRHVVQLRAQEEFGQGEWSEWSPEAMG"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A murine Fv, mAb6D8 (IGHV14/IGKV3-Kappa), targeting the Merozoite surface protein 2 of Plasmodium falciparum. Merozoite surface protein 2 is an intrinsically disordered, membrane-anchored antigen that may play a role in merozoite attachment to the erythrocyte. The antibody is designed to recognize a conserved N-terminal epitope of MSP2 on the parasite surface, with recognition modulated by transient interactions with polymorphic regions flanking the conserved epitope, conferring strain-specific binding despite targeting a fully conserved sequence.", "target_protein": "QVQLQQSGDELVKPGASVKLSCTVSIHWMKQRPEQGLEWIGRKYAPKFQDKATMTADTSSNTAYLQLSSLASEDAAVYYCWGQGTLVTVSAGFNIKDDFIDPANGYTATYGVAY", "metadata": {"pdb_id": "4qxt", "light_chain_seq": "DIVLTQSPASLAVSLGQRATISCKASQSVDHDGDSYMNWFQQKPGQSPKLLIYAASNLESGIPARFSGSGSGTDFTLNIHPVEEEDAATYYCQQTNEDPYTFGGGTKLEIK", "cdrh1_seq": "GFNIKDDF", "cdrh2_seq": "IDPANGYT", "cdrh3_seq": "ATYGVAY", "cdrl1_seq": "QSVDHDGDSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQTNEDPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 102]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "4r3s", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "mAb6D8", "antibody_format": "Fv", "heavy_subclass": "IGHV14", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Merozoite surface protein 2, Plasmodium falciparum", "target_domain": null, "functional_role": "other", "evidence_quote": "antibodies able to recognize the N-terminal region of MSP2 on the merozoite surface"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 11417, 16, 7032, 1016, 1007, 1025, 12, 20733, 7390, 1006, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 6902, 26553, 3154, 2213, 22, 1927, 15663, 13098, 18, 6902, 26553, 3154, 2213, 22, 1977, 1925, 20061, 13885, 16, 3260, 17, 17199, 4730, 1988, 2278, 3918, 43, 2770, 1922, 6902, 26553, 8576, 1942, 1920, 15469, 18, 1920, 3533, 1977, 4609, 1942, 9967, 43, 5305, 56, 17, 4262, 10095, 1927, 22064, 1028, 1990, 1920, 8652, 3154, 16, 1956, 5708, 9985, 2007, 6809, 3719, 1956, 14240, 3451, 12679, 1920, 5305, 10095, 16, 21510, 3943, 17, 2487, 2743, 4281, 5133, 43, 5437, 5305, 3244, 18, 3], "antigen": ["NAYNMSIRRS"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, PN-SIA28 (IGHV3/IGKV1-Kappa), targeting the Hemagglutinin of Influenza A virus. Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and internalization, and is responsible for membrane fusion during viral entry. The antibody is designed as a broadly neutralizing antibody targeting a conserved epitope in the fusion domain, capable of inhibiting membrane fusion across diverse influenza A subtypes including group 1, group 2, and bat-origin H17 and H18 HAs.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVAGYYADSVKGRFTISRDSSKSTLYLQMNSLRPEDTAVYYCWGQGTTVTVSGFPFSSYGVSYDGSYKARPSAIFGIYIILNGLDV", "metadata": {"pdb_id": "7wvd", "light_chain_seq": "EIVLTQSPSSVSASVGDRVTITCRATQGISSWLAWYQQKPGKPPKLLIFGASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYFCQQAHSFPLTFGGGTKVEIK", "cdrh1_seq": "GFPFSSYG", "cdrh2_seq": "VSYDGSYK", "cdrh3_seq": "ARPSAIFGIYIILNGLDV", "cdrl1_seq": "QGISSW", "cdrl2_seq": "GAS", "cdrl3_seq": "QQAHSFPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7wvd", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "PN-SIA28", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "inhibits membrane fusion mediated by bat-origin H17 and H18 HAs"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 7594, 17, 26352, 4839, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 12071, 16, 1930, 1977, 5061, 1958, 3260, 5289, 2409, 4324, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 43, 5305, 10095, 1922, 1920, 5289, 3418, 16, 7131, 1927, 7918, 3260, 5289, 3436, 6445, 7108, 43, 8160, 2710, 2210, 21, 16, 2210, 22, 16, 1930, 11579, 17, 4853, 9169, 1027, 1930, 9169, 1025, 2258, 18, 3], "antigen": ["GLFGAIAGFIENGWQGLIDGWYGFRHQNAEGTGTAADLKSTQAAIDQINGKLNRLIEKTNEKYHQIEKEFEQVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDVTDSEMNKLFERVRRQLRENAEDQGNGCFEIFHQCDNNCIESIRNGTYDHNIYRDEAINNRIK", "GNPVICLGHHAVENGTSVKTLTDNHIEVVSAKELVETNHINELCPSPLKLVDGQDCDLINGALGSPGCDHLQDTTWDVFIERPTAMDTCYPFDVPDYQSLRSILASSGSLEFIAEQFTWNGVTVDGSSSACLRGGRNGFFTRLNWLTRVKNGNYGPINVTKENTGSYVRLYLWGVHHPSSDTEQTDLYKVATGRVTVSTRSDQISIIPNIGSRPRVRNQSGRISIYWTLVNPGDSIIFNSIGNLIAPRGHYKINKSTKGTVLKSDKKIGSCTSPCLTDKGSIQSDKPFQNVSRIAIGNCPKYVKQGSLMLATGMRNIP"]} {"modality_type": "antibody", "text": "Output the HCDRs for an antibody that performs this function: A human Fab, PGZL1 (IGHV1/IGKV3-Kappa), targeting the membrane-proximal external region (MPER) of the Envelope glycoprotein gp160 of Human immunodeficiency virus 1. The Envelope glycoprotein gp160 oligomerizes into trimers and mediates viral attachment to host cells and membrane fusion. The antibody is designed as a broadly neutralizing antibody targeting the MPER epitope (residues 671\u2013683) in the context of the viral membrane, with binding that engages both the peptide epitope and lipid head groups of the membrane.", "target_protein": "EVQLVQSGGEVKRPGSSVTVSCKATFNWVRQAPGQGPEWMGGNYGQKFQGRLTIRADKSTTTVFLDLSGLTSADTATYYCWGQGTVITVSSAGGTFSTLAIVPLFSIVAREGEGWFGKPLRAFEF", "metadata": {"pdb_id": "6o3g", "light_chain_seq": "DVVMTQSPGTLSLSPGERATLSCRASQSVSGGALAWYQQKPGQAPRLLIYDTSSRPTGVPGRFSGSGSGTDFSLTISRLEPEDFAVYYCQQYGTSQSTFGQGTRLEIKRT", "cdrh1_seq": "GGTFSTLA", "cdrh2_seq": "IVPLFSIV", "cdrh3_seq": "AREGEGWFGKPLRAFEF", "cdrl1_seq": "QSVSGGA", "cdrl2_seq": "DTS", "cdrl3_seq": "QQYGTSQST", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "6mto", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "PGZL1", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus 1", "target_domain": "MPER; binding to GalCer", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibody from an HIV-infected person that recognizes the membrane-proximal external region (MPER)"}}}, "tokenized_instruction": [2, 6647, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 17436, 2052, 2347, 30, 43, 2616, 6914, 16, 5306, 26262, 1009, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 1927, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 21, 18, 1920, 11262, 11424, 4882, 16954, 13034, 4517, 2460, 28220, 1930, 10412, 4324, 8576, 1942, 4423, 2094, 1930, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 5438, 1915, 10095, 12, 4248, 4838, 1009, 229, 5117, 1010, 13, 1922, 1920, 4491, 1927, 1920, 4324, 3260, 16, 1956, 2743, 1988, 11580, 1036, 2321, 1920, 4207, 10095, 1930, 4486, 4469, 2671, 1927, 1920, 3260, 18, 3], "antigen": ["NWFDITNWLWYIKKKK"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A murine Fab (IGHV1/IGKV4-Kappa) targeting the Leukocidin AB complex of Staphylococcus aureus. Leukocidins are pore-forming toxins that damage host cells during infection. The antibody is designed to neutralize pore-forming leukocidins as part of a multivalent mAbtyrin fusion construct, conferring protection against S. aureus infection.", "target_protein": "EVQLQQSGAELVKPGASVKISCKASMNWLKQRPGKGLEWIGRNYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCWGQGTSVTVSSAGYAFSSSWIYPGDGDTARYGYDYDGEYYYAMDY", "metadata": {"pdb_id": "7t87", "light_chain_seq": "DIVMTQSPTTMAASPGERITITCSAHSNLISNYLHWYQQKPGFSPKLLIYRTSNLASGVPARFSGSGSGTSYSLTIGTMEAEDVATYFCQQGSSIPFTFGSGTKLEIKRT", "cdrh1_seq": "GYAFSSSW", "cdrh2_seq": "IYPGDGDT", "cdrh3_seq": "ARYGYDYDGEYYYAMDY", "cdrl1_seq": "SNLISNY", "cdrl2_seq": "RTS", "cdrl3_seq": "QQGSSIPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "8gkl", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Leukocidin AB complex, Staphylococcus aureus", "target_domain": null, "functional_role": "other", "evidence_quote": "neutralizes pore-forming leukocidins via fusion with anti-toxin centyrins"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1920, 5104, 2240, 22816, 2186, 2796, 1927, 13452, 8849, 18, 5104, 2240, 22816, 1036, 2032, 8554, 17, 7402, 13599, 1988, 4293, 4423, 2094, 2409, 2909, 18, 1920, 3533, 1977, 4609, 1942, 25885, 8554, 17, 7402, 5104, 2240, 22816, 1036, 1966, 3131, 1927, 43, 5738, 16896, 7032, 3145, 5572, 5289, 6377, 16, 21510, 6202, 3316, 61, 18, 8849, 2909, 18, 3], "antigen": ["GDTKMYTRTATTSDSQKNITQSLQFNFLTEPNYDKETVFIKAKGTIGSGLRILDPNGYWNSTLRWPGSYSVSIQNVDDNNNTNVTDFAPKNQDESREVKYTYGYKTGGDFSINRGGLTGNITKESNYSETISYQQPSYRTLLDQSTSHKGVGWKVEAHLINNMGHDHTRQLTNDSDNRTKSEIFSLTRNGNLWAKDNFTPKDKMPVTVSEGFNPEFLAVMSHDKKDKGKSQFVVHYKRSMDEFKIDWNRHGFWGYWSGENHVDKKEEKLSALYEVDWKTHNVKFVKVLND", "GKNGKITKRTETVYDEKTNILQNLQFDFIDDPTYDKNVLLVKKQGSIHSNLKFESHKEEKNSNWLKYPSEYHVDFQVKRNRKTEILDQLPKNKISTAKVDSTFSYSSGGKFDSTKGIGRTSSNSYSKTISYNQQNYDTIASGKNNNWHVHWSVIANDLKYGGEVKNRNDELLFYRNTRIATVENPELSFASKYRYPALVRSGFNPEFLTYLSNEKSNEKTQFEVTYTRNQDILKNRPGIHYAPPILEKNKDGQRLIVTYEVDWKNKTVKVVDKYSDDNKPYKE"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human Fab (IGHV3/IGKV1-Kappa), the anti-FIXa arm of the bispecific antibody Mim8, targeting Coagulation factor IX of Homo sapiens. Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca\u00b2\u207a ions, phospholipids, and factor VIIIa. The antibody is designed to function as an activated factor VIII mimetic by assembling with factor X on the phospholipid membrane and allosterically enhancing the proteolytic activity of activated factor IX, thereby restoring hemostasis in hemophilia A, binding within the Peptidase S1. Generate the corresponding HCDRs.", "target_protein": "EVQLVESGGGLVQPGRSLRLSCAASMHWVRQVPGKGLEWVSGGYVKSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYCWGQGTLVTVSSAGFTFHDYAISWRGDIGVKSYGSGSFYNAFDS", "metadata": {"pdb_id": "7ahv", "light_chain_seq": "DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKFLIYKASKLERGTPSRFSGSGDGTEFSLTISSLQPDDFATYYCLEYSSYIRTFGQGTKVEIKRT", "cdrh1_seq": "GFTFHDYA", "cdrh2_seq": "ISWRGDIG", "cdrh3_seq": "VKSYGSGSFYNAFDS", "cdrl1_seq": "QSISSW", "cdrl2_seq": "KAS", "cdrl3_seq": "LEYSSYIRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7ahv", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Coagulation factor IX, Homo sapiens", "target_domain": "Peptidase S1", "functional_role": "other", "evidence_quote": "bispecific antibody (Mim8) assembled efficiently with FIXa and FX on membranes, and supported activation"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 1920, 2246, 17, 4011, 1019, 6011, 1927, 1920, 7266, 10231, 3533, 6571, 1025, 16, 5133, 12441, 2991, 13848, 1927, 16350, 27974, 18, 2991, 13848, 1977, 43, 6111, 53, 17, 3100, 3582, 2213, 1988, 17241, 1922, 1920, 7598, 3374, 1927, 2877, 12441, 2007, 15025, 2991, 66, 1942, 2496, 3500, 2386, 1922, 1920, 2990, 1927, 2332, 1189, 1323, 6982, 16, 15619, 16, 1930, 2991, 18675, 1019, 18, 1920, 3533, 1977, 4609, 1942, 2347, 1966, 1925, 4128, 2991, 18675, 24878, 2007, 26358, 1956, 2991, 66, 1990, 1920, 14608, 3260, 1930, 14772, 2169, 9221, 1920, 12712, 2455, 1927, 4128, 2991, 13848, 16, 6113, 20174, 23963, 1922, 3243, 19740, 43, 16, 2743, 2651, 1920, 24050, 4062, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGRSALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human Fab, PN-SIA28 (IGHV3/IGKV1-Kappa), targeting the Hemagglutinin of Influenza A virus. Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and internalization, and functions as a class I viral fusion protein responsible for penetration into the cell cytoplasm by mediating membrane fusion. The antibody is designed as a broadly neutralizing antibody targeting the conserved stem region of HA, capable of neutralizing divergent group 1 and group 2 influenza A subtypes including endemic strains and emerging bat influenza viruses, and functioning by inhibiting HA-mediated membrane fusion and blocking HA0 maturation. Please generate the HCDRs for this antibody.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVAGYYADSVKGRFTISRDSSKSTLYLQMNSLRPEDTAVYYCWGQGTTVTVSGFPFSSYGVSYDGSYKARPSAIFGIYIILNGLDV", "metadata": {"pdb_id": "8gv6", "light_chain_seq": "EIVLTQSPSSVSASVGDRVTITCRATQGISSWLAWYQQKPGKPPKLLIFGASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYFCQQAHSFPLTFGGGTKVEIK", "cdrh1_seq": "GFPFSSYG", "cdrh2_seq": "VSYDGSYK", "cdrh3_seq": "ARPSAIFGIYIILNGLDV", "cdrl1_seq": "QGISSW", "cdrl2_seq": "GAS", "cdrl3_seq": "QQAHSFPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7wvd", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "PN-SIA28", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Hemagglutinin H14, Influenza A virus (A/long-tailed duck/Wisconsin/10OS3912/2010(H14N6))", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing activity against group 1 and group 2 IAV strains"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 7594, 17, 26352, 4839, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 12071, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 12006, 2460, 1920, 2024, 5239, 2007, 10239, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 5305, 4402, 3031, 1927, 2118, 16, 7131, 1927, 12130, 13609, 2210, 21, 1930, 2210, 22, 7108, 43, 8160, 2710, 12310, 4046, 1930, 8484, 11579, 7108, 6241, 16, 1930, 7295, 2007, 7918, 2118, 17, 3434, 3260, 5289, 1930, 7472, 2118, 1008, 7655, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["GLFGAIAGFIENGWQGLIDGWYGFRHQNAEGTGTAADLKSTQAAIDQINGKLNRLIEKTNEKYHQIEKEFEQVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDVTDSEMNKLFERVRRQLRENAEDQGNGCFEIFHQCDNNCIESIRNGTYDHNIYRDEAINNRIK", "GNPVICLGHHAVENGTSVKTLTDNHIEVVSAKELVETNHINELCPSPLKLVDGQDCDLINGALGSPGCDHLQDTTWDVFIERPTAMDTCYPFDVPDYQSLRSILASSGSLEFIAEQFTWNGVTVDGSSSACLRGGRNGFFTRLNWLTRVKNGNYGPINVTKENTGSYVRLYLWGVHHPSSDTEQTDLYKVATGRVTVSTRSDQISIIPNIGSRPRVRNQSGRISIYWTLVNPGDSIIFNSIGNLIAPRGHYKINKSTKGTVLKSDKKIGSCTSPCLTDKGSIQSDKPFQNVSRIAIGNCPKYVKQGSLMLATGMRNIP"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab, ADI-14359 (IGHV2/IGKV1-Kappa), targeting the postfusion Fusion glycoprotein F0 of Human respiratory syncytial virus. The Fusion glycoprotein F0 is a class I viral fusion protein that mediates fusion of viral and cellular membranes during entry. This antibody is an infant-derived, non-neutralizing antibody directed against antigenic site I, which is preferentially exposed on the postfusion conformation and represents a major component of the infant antibody response to RSV infection.", "target_protein": "QVTLRESGPALVKPTQTLTLTCTFSVSWIRQPPGKALEWLARYYSTSLKTRLTISKDTSKNQVVLTMTNMDPVDTATYYCWGQGTLVTVSSAGFSLSTSGMCIDWDDDKARATNYDSSGYYSLYFDY", "metadata": {"pdb_id": "6apb", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPYTFGGGTKVEIKRT", "cdrh1_seq": "GFSLSTSGMC", "cdrh2_seq": "IDWDDDK", "cdrh3_seq": "ARATNYDSSGYYSLYFDY", "cdrl1_seq": "QSISSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSYSTPYT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 114]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6apb", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ADI-14359", "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Fusion glycoprotein F0, Human respiratory syncytial virus", "target_domain": null, "functional_role": "other", "evidence_quote": "site I-directed antibodies are typically non-neutralizing"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 2041, 1033, 17, 13370, 7308, 12, 20733, 15755, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 2753, 9049, 5289, 11424, 17930, 1927, 2616, 5481, 29988, 3413, 18, 1920, 5289, 11424, 17930, 1977, 43, 2921, 51, 4324, 5289, 2213, 1988, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2409, 6904, 18, 2052, 3533, 1977, 1925, 8125, 17, 3595, 16, 2447, 17, 12130, 3533, 6554, 3316, 14606, 3200, 51, 16, 2154, 1977, 10662, 4616, 1990, 1920, 2753, 9049, 7748, 1930, 4972, 43, 3044, 4594, 1927, 1920, 8125, 3533, 2644, 1942, 12390, 2909, 18, 3], "antigen": ["NITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLG", "NITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLGL"]} {"modality_type": "antibody", "text": "Output the HCDRs for an antibody that performs this function: A human Fab, KA30L (IGHV4/IGKV1-Kappa), targeting isoform 2B of GTPase KRas. GTPase KRas is a signal transducer in the Ras-MAPK signaling pathway that regulates cell proliferation and survival, and plays a role in promoting oncogenic events. This antibody forms a complex with the GDP-bound form of KRas in the presence of the cyclic peptide inhibitor LUNA18.", "target_protein": "QVQLQESGPGLVKPSETLSLTCAVSWGWIRQPPGKGLEWIGSYYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCWGQGTLVTVSSAGYSISSGYYIYHSGSTARQRYWSKSYFRP", "metadata": {"pdb_id": "7yv1", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSDSYPLTFGGGTKVEIKRT", "cdrh1_seq": "GYSISSGYY", "cdrh2_seq": "IYHSGST", "cdrh3_seq": "ARQRYWSKSYFRP", "cdrl1_seq": "QSISSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSDSYPLT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7yv1", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "KA30L", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Isoform 2B of GTPase KRas, Homo sapiens", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 6647, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 17436, 2052, 2347, 30, 43, 2616, 6914, 16, 9580, 4294, 1024, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 6174, 5751, 1927, 14809, 11083, 18, 14809, 11083, 1977, 43, 2733, 14848, 1922, 1920, 6520, 17, 7859, 3197, 3374, 1988, 7014, 2024, 4031, 1930, 3298, 16, 1930, 5705, 43, 2770, 1922, 7356, 11446, 3916, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 15217, 17, 4124, 2386, 1927, 11083, 1922, 1920, 2990, 1927, 1920, 9821, 4207, 4106, 24123, 4904, 1025, 18, 3], "antigen": ["STEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab, ConBA-998 (IGHV1/IGKV3-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2, specifically the Omicron BA.1 variant. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes through class I viral fusion protein mechanisms. The antibody is designed as a neutralizing antibody elicited by primary Omicron BA.1 infection, binding within the BetaCoV S1-CTD and triggering S1 subunit shedding from the spike protein.", "target_protein": "VQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "9lbs", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIK", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 114]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ConBA-998", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "BetaCoV S1-CTD", "functional_role": "neutralizing", "evidence_quote": "IGHV3-66-encoding monoclonal nAb elicited by primary infection with BA.1"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 16, 1962, 7972, 17, 4922, 1025, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 16, 4475, 1920, 7254, 1935, 2830, 6813, 18, 21, 6031, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 2921, 51, 4324, 5289, 2213, 3531, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 9856, 2007, 3065, 7254, 1935, 2830, 6813, 18, 21, 2909, 16, 2743, 2651, 1920, 4666, 4879, 1020, 4062, 17, 15898, 1930, 14074, 4062, 5903, 16802, 2037, 1920, 10429, 2213, 18, 3], "antigen": ["PFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFEL"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A human Fab, CR12044 (IGHV1/IGLV1-Lambda), targeting the engineered Neuraminidase of Influenza A virus (A/California/07/2009 H1N1). Neuraminidase catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates to facilitate virus release and spread. The antibody is designed as a neutralizing antibody targeting the NA active site through receptor mimicry, binding within the Head of neuraminidase. Generate the corresponding HCDRs.", "target_protein": "EVQLVQSGSEVRKPGSTVKVSCKGSIHWVRQAPGQGLRWMGGNHAQEFQGRATITADESTTTAYLELSSLRSEDSAVYYCWGQGTTVTVSSGGAFRTSVIIPTLDTAATDYGGNSDRLGSYSFAFDV", "metadata": {"pdb_id": "9o4o", "light_chain_seq": "SVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVNWYQQLPGTAPKLLIYSNNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNGWVFGGGTQLTVL", "cdrh1_seq": "GGAFRTSV", "cdrh2_seq": "IIPTLDTA", "cdrh3_seq": "ATDYGGNSDRLGSYSFAFDV", "cdrl1_seq": "SSNIGSNT", "cdrl2_seq": "SNN", "cdrl3_seq": "AAWDDSLNGWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[24, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "9o4o", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CR12044", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Neuraminidase, Influenza A virus (A/California/07/2009 H1N1)", "target_domain": "Head of neuraminidase", "functional_role": "neutralizing", "evidence_quote": "CR12044 targeted and blocked the NA active site"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 2345, 9363, 6609, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 11091, 29831, 1927, 7108, 43, 3413, 12, 43, 19, 10191, 19, 6627, 19, 3712, 15355, 13, 18, 29831, 17097, 1920, 6025, 1927, 4262, 20436, 2687, 4248, 2037, 4324, 1930, 3689, 4235, 30378, 2209, 1942, 6628, 3413, 4012, 1930, 6441, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 4049, 3500, 3200, 2596, 3148, 10223, 6907, 16, 2743, 2651, 1920, 4469, 1927, 29831, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["VKLAGNSSLCPVSGWAPLSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSVPIGSVPSPYNARFESIAWSASACHDGINWLTIGITGPDNGAVAILKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVMHPELTGLDCIVPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTIDK"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A murine Fab, 5B3 (IGHV5/IGKV12-Kappa), targeting the engineered prefusion Fusion glycoprotein F0 of Nipah virus. The Fusion glycoprotein F0 is a class I viral fusion protein that directs fusion of viral and cellular membranes leading to delivery of the nucleocapsid into the cytoplasm. The antibody is designed as a cross-neutralizing antibody against Nipah and Hendra viruses that recognizes a quaternary epitope on the prefusion F trimer and prevents fusogenic conformational changes by locking F in the prefusion state. Please generate the HCDRs for this antibody.", "target_protein": "EVQLVESGGGLVKPGGSLKLSCAASMSWVRQTPEKRLEWVAMYYPDSVKGRFTISRDNAKNTLYLQMSSLRSEDTAMYYCWGQGTLVTVSSAGFTFSSYDISSGGSYSARQGDYAWFAY", "metadata": {"pdb_id": "6tys", "light_chain_seq": "DIQMTQSPASQSASLGESVTITCLASQTIGTWLAWYQQKPGKSPQLLIYAATSLADGVPSRFSGSGSGTKFSFKISSLQAEDFVSYYCQQFYSTPFTFGGGTKLEIK", "cdrh1_seq": "GFTFSSYD", "cdrh2_seq": "ISSGGSYS", "cdrh3_seq": "ARQGDYAWFAY", "cdrl1_seq": "QTIGTW", "cdrl2_seq": "AAT", "cdrl3_seq": "QQFYSTPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6tys", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "5B3", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV12", "is_engineered": true, "target_antigen": "Fusion glycoprotein F0, Nipah virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "potently inhibited NiV and HeV infection by locking F in the prefusion conformation"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 7807, 1010, 12, 20733, 1020, 1015, 19, 7021, 1040, 7390, 1028, 17, 12093, 13, 16, 5133, 1920, 11091, 9328, 2670, 5289, 11424, 17930, 1927, 18786, 5945, 3413, 18, 1920, 5289, 11424, 17930, 1977, 43, 2921, 51, 4324, 5289, 2213, 1988, 28351, 5289, 1927, 4324, 1930, 3689, 5726, 4523, 1942, 4868, 1927, 1920, 2797, 28712, 1960, 2460, 1920, 5239, 18, 1920, 3533, 1977, 4609, 1966, 43, 3567, 17, 12130, 3533, 3316, 18786, 5945, 1930, 26160, 5524, 6241, 1988, 16197, 43, 21920, 10095, 1990, 1920, 9328, 2670, 48, 20085, 1930, 10299, 10630, 3880, 8523, 2840, 2007, 24536, 48, 1922, 1920, 9328, 2670, 3360, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["ILHYEKLSKIGLVKGVTRKYKIKSNPLTKDIVIKMIPNVSNMSQCTGSVMENYKTRLNGILTPIKGALEIYKNCTHDLGVIMAGVCIGIATAAQITAGVALYEAMKNADNINKLKSSIESTNEAVVKLQETAEKTVYVLTALQDYINTNLVPTIDKISCKQTELSLDLALSKYLSDLLFVFGPNLQDPVSNSMTIQAISQAFGGNYETLLRTLGYATEDFDDLLESDSITGQIIYVDLSSYYIIVRVYFPILTEIQQAYIQELLPVSFNNDNSEWISIVPNFILVRNTLISNIEIGFCLITKRSVICNQDYATPMTNNMRECLTGSTEKCPRELVVSSHVPRFALSNGVLFANCISVTCQCQTTGRAISQSGEQTLLMIDNTTCPTAVLGNVIISLGKYLGSVNYNSEGIAIGPPVFTDKVDISSQISSMNQSLQQSKDYIKEAQRL"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A human Fab, N60P23 (IGKV1-Kappa), targeting the clade A/E 93TH057 HIV-1 gp120 core of Human immunodeficiency virus 1. The gp120 glycoprotein mediates viral attachment and entry into CD4+ T cells. The antibody is designed as a neutralizing antibody targeting the CD4 binding site (CD4bs), a highly conserved epitope that enables broad neutralization across diverse HIV variants. Generate the corresponding HCDRs.", "target_protein": "QIELVQSGTEVKRPGASVRISCASSIHWVRQAPGRGLEWMGWNYSGRFQGRVTMTRDIYTETSFMVLSGLRSDDSAIYFCWGQGTLVTVTAAGYRFTNYFMNPLHGGVTRGRDGYDDGFHP", "metadata": {"pdb_id": "5wb9", "light_chain_seq": "SPSTLYASVGDKITITCRSSQSGWKAWYQQKPGKAPKLLIYKSSILETGVPSRFIGSDSGTEFTLTISSLQPDDFATYYCQHFETFGQGTRVQVRRT", "cdrh1_seq": "GYRFTNYF", "cdrh2_seq": "MNPLHGGV", "cdrh3_seq": "TRGRDGYDDGFHP", "cdrl1_seq": "QSGW", "cdrl2_seq": "KSS", "cdrl3_seq": "QHFET", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[20, 23]", "cdrl2_pos": "[41, 43]", "cdrl3_pos": "[80, 84]", "cdrh3_split": "val", "cdrh3_cluster": "5wb9", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "N60P23", "antibody_format": "Fab", "heavy_subclass": null, "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "clade A/E 93TH057 HIV-1 gp120 core, Human immunodeficiency virus 1", "target_domain": "CD4 binding site (CD4bs)", "functional_role": "neutralizing", "evidence_quote": "HIV-neutralizing antibody achieves near pan-neutralizing activity through recognition of a highly conserved region"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 29077, 1008, 5991, 1010, 12, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11315, 43, 19, 47, 6156, 1963, 15264, 1027, 3525, 17, 21, 16102, 4728, 1927, 2616, 13141, 3413, 21, 18, 1920, 16102, 11424, 10412, 4324, 8576, 1930, 6904, 2460, 4095, 15, 62, 2094, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 4095, 2743, 3200, 12, 4095, 2083, 13, 16, 43, 3626, 5305, 10095, 1988, 10217, 4949, 14377, 3436, 6445, 3525, 4936, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["WKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCIMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A human Fab, WCSL 129 (IGHV3/IGLV1-Lambda), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the host cell membrane by interacting with the ACE2 receptor, initiating infection. The antibody is designed as a neutralizing antibody that blocks SARS-CoV-2 virus entry by preventing receptor engagement, binding within the Receptor-binding domain (RBD).", "target_protein": "VQLLESGGGLVQPGGSLRLSCAASMTWVRQAPGKGLEWVSAYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTMVTVSSAGFTFSRFAISGSGGSTAKVGWGAFDI", "metadata": {"pdb_id": "7mzj", "light_chain_seq": "SVLTQPPSASGTPGQSVSISCSGTYSNIGSNPVNWYQQVPGTAPKLLIYANDQRPSGVPDRFSGSKSATSAFLAIGGLQSEDDADYYCSTWDDSLPGPLFGGGTKLTVLGQ", "cdrh1_seq": "GFTFSRFA", "cdrh2_seq": "ISGSGGST", "cdrh3_seq": "AKVGWGAFDI", "cdrl1_seq": "YSNIGSNP", "cdrl2_seq": "AND", "cdrl3_seq": "STWDDSLPGPL", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 104]", "cdrl1_pos": "[24, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "7mzi", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "WCSL 129", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "potent human monoclonal antibodies that block SARS-CoV-2 virus entry"}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 14888, 1036, 1024, 9367, 12, 20733, 1020, 1010, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 1920, 8298, 1028, 3148, 16, 12410, 2909, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 20466, 17, 6083, 17, 22, 3413, 6904, 2007, 8444, 3148, 9577, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 3], "antigen": ["NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPGS"]} {"modality_type": "antibody", "text": "A human Fab, 1G1 (IGHV1/IGLV3-Lambda), targeting the engineered mature secreted glycoprotein G of Respiratory syncytial virus A2. The Major surface glycoprotein G attaches the virion to the host cell membrane by interacting with heparan sulfate to initiate infection, and helps the virus escape antibody-dependent restriction by acting as an antigen decoy and modulating leukocyte activity. This antibody forms a complex with the central conserved region of RSV G, recognizing a conformational epitope formed by the N-terminal region and cysteine loop of the CCD. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "QVHLVQSGVEVKKPGASVRVSCKASITWVRQAPGRGLEWVGWSYAQIFHGRVTMTTDTSTNTAYMELRSLRSDDTAMYYCWGQGTLVSVSSAGYTFATYGITPYNDRTARNHCNFYHDFWSGLDY", "metadata": {"pdb_id": "9cqa", "light_chain_seq": "SFELTQPPSVSVSPGQTARITCSGDALPKQYVYWYQQKPGQAPVLVIYKTTERPSGIPERFSDSSSGTTVTLTISAAQAEDEADYYCQSVDSSGTYVFGIGTKVTVLGR", "cdrh1_seq": "GYTFATYG", "cdrh2_seq": "ITPYNDRT", "cdrh3_seq": "ARNHCNFYHDFWSGLDY", "cdrl1_seq": "ALPKQY", "cdrl2_seq": "KTT", "cdrl3_seq": "QSVDSSGTYV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9cqa", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "1G1", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV3", "is_engineered": true, "target_antigen": "Major surface glycoprotein G, Respiratory syncytial virus A2", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 43, 2616, 6914, 16, 15957, 1009, 12, 20733, 7390, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 5133, 1920, 11091, 6665, 8366, 11424, 49, 1927, 5481, 29988, 3413, 8595, 18, 1920, 3044, 3154, 11424, 49, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 22024, 8767, 1942, 11051, 2909, 16, 1930, 12612, 1920, 3413, 11781, 3533, 17, 3100, 7587, 2007, 8290, 1966, 1925, 4730, 25164, 1930, 10871, 11864, 2455, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 4101, 5305, 3031, 1927, 12390, 49, 16, 15667, 43, 8523, 10095, 5333, 2007, 1920, 56, 17, 4262, 3031, 1930, 8666, 5881, 1927, 1920, 16498, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["NDFHFEVFNFVPCSICSNNPTCWAICKR"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab (IGHV1/IGKV3-Kappa), S309, targeting the Spike protein S1 of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors including ACE2, TFRC, GRM2, NRP1/NRP2, ASGR1, and integrin, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. This antibody forms a complex with the Spike protein S1 within the Receptor-binding domain (RBD).", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7xck", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike protein S1, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 6080, 13192, 16, 5133, 1920, 10429, 2213, 4062, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 2710, 8298, 1028, 16, 26817, 1030, 16, 2398, 8224, 16, 5214, 5113, 19, 5214, 5991, 16, 1966, 2299, 1009, 16, 1930, 8920, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 2213, 4062, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 3], "antigen": ["PTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPC"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab, MOR04252 (IGHV3/IGLV3-Lambda), targeting human Granulocyte-macrophage colony-stimulating factor (GM-CSF). GM-CSF is a cytokine that stimulates the growth and differentiation of hematopoietic precursor cells from various lineages, including granulocytes, macrophages, eosinophils and erythrocytes. The antibody is designed as a neutralizing antibody that blocks GM-CSF binding to its receptors through engagement of a conformational epitope.", "target_protein": "QVQLVESGGGLVQPGGSLRLSCAASMNWVRQAPGKGLEWVSGYYAASVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTFSSYWIENKYAGGATARGFGTDF", "metadata": {"pdb_id": "5d72", "light_chain_seq": "DIELTQPPSVSVAPGQTARISCSGDSIGKKYAYWYQQKPGQAPVLVIYKKRERFSGSNSGNTATLTISGTQAEDEADYYCSSWDSTGLVFGGGTKLTVLGQ", "cdrh1_seq": "GFTFSSYW", "cdrh2_seq": "IENKYAGGAT", "cdrh3_seq": "ARGFGTDF", "cdrl1_seq": "SIGKKY", "cdrl2_seq": "KK", "cdrl3_seq": "SSWDSTGLV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 105]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 49]", "cdrl3_pos": "[80, 88]", "cdrh3_split": "val", "cdrh3_cluster": "5c7x", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "MOR04252", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "Granulocyte-macrophage colony-stimulating factor, Homo sapiens", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing anti-human GM-CSF antibody"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 16, 2803, 14743, 4198, 1028, 12, 20733, 1020, 1010, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 5133, 2616, 19235, 17, 8088, 8271, 17, 9868, 2991, 12, 5711, 17, 6399, 13, 18, 5711, 17, 6399, 1977, 43, 6137, 1988, 11803, 1920, 2905, 1930, 4155, 1927, 9960, 7897, 2094, 2037, 3425, 10439, 16, 2710, 22144, 16, 5205, 16, 15854, 1930, 14161, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 5711, 17, 6399, 2743, 1942, 2496, 4086, 2596, 9577, 1927, 43, 8523, 10095, 18, 3], "antigen": ["PSTQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEP"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (B.1.617.1 kappa variant). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding and proteolytic cleavage. The antibody is designed as a neutralizing antibody targeting the receptor-binding domain.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7soc", "light_chain_seq": "IVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVE", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[25, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "monoclonal antibodies via alteration of key antigenic sites"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 44, 18, 21, 18, 5473, 1027, 18, 21, 12093, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 1930, 12712, 6404, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 3148, 17, 2743, 3418, 18, 3], "antigen": ["FPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVCPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSTPCNGVQGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human Fab (IGHV3/IGLV3-Lambda) targeting the H3K9me3 peptide, a synthetic construct derived from Histone H3.1. Histone H3.1 is a core component of the nucleosome and plays a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability through post-translational modifications. The antibody is designed to recognize trimethylated lysine residues on histone H3 with exquisite specificity for epigenetics applications. What would the HCDRs be?", "target_protein": "EVQLVETGGGVVQPGRSLRLSCTASMSWVRQAPGKGLEWVADYYIDAVKGRFTISRDNAKSSLYLQMNSLGAEDTAVYYCWGRGTLVTVSSAGFTFRDYWINPDGITRAREFHSGLGWHFDL", "metadata": {"pdb_id": "4yhp", "light_chain_seq": "SYVLTQPPSVSVAPGQTARITCGGTNIGDISVHWYQQRPGQAPLVVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDDSINAYVFGTGTKVTVLRT", "cdrh1_seq": "GFTFRDYW", "cdrh2_seq": "INPDGITR", "cdrh3_seq": "AREFHSGLGWHFDL", "cdrl1_seq": "NIGDIS", "cdrl2_seq": "DDS", "cdrl3_seq": "QVWDDSINAYV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 97]", "cdrh3_split": "val", "cdrh3_cluster": "4yhz", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "H3K9me3 peptide, synthetic construct", "target_domain": null, "functional_role": "other", "evidence_quote": "antibodies to trimethylated lysine residues on histone H3, important epigenetic marks"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 28961, 1020, 1010, 17, 18279, 13, 5133, 1920, 28877, 4207, 16, 43, 6830, 6377, 3595, 2037, 6632, 8170, 18, 21, 18, 6632, 8170, 18, 21, 1977, 43, 4728, 4594, 1927, 1920, 14914, 1930, 5705, 43, 4101, 2770, 1922, 3213, 3640, 16, 2678, 5059, 16, 2678, 5158, 16, 1930, 9220, 5057, 2596, 2753, 17, 8414, 6920, 18, 1920, 3533, 1977, 4609, 1942, 9967, 21849, 1981, 9082, 4248, 1990, 6632, 8170, 1956, 1975, 17478, 4896, 1958, 30122, 5990, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["ARTKQTARST"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A murine Fab, vFP1.01 (IGHV1/IGKV1-Kappa), targeting the Envelope glycoprotein gp41 of Human immunodeficiency virus 1. The Envelope glycoprotein gp160 is proteolytically cleaved to produce gp120 and gp41, which mediate viral entry through CD4 and coreceptor binding and membrane fusion. The antibody is designed as a vaccine-elicited neutralizing antibody targeting the fusion peptide, a conserved epitope region that mediates viral escape through mutations in the N-terminal fusion peptide residues.", "target_protein": "QVQLQQSGTELVWPGTSVTLSCKASIHWVKQTPVHGLEWIGAAYNQKFRGKAILTADKSSSTAYMDLRRLTSEDSAVYYCWGTGTTVTVGYTFTDYEIVPKTGYTTRLRNYWYFDV", "metadata": {"pdb_id": "6cuf", "light_chain_seq": "DFLMAQTPLSLPVSLGDQASISCRSSQSIVYSDGNTYLEWYLQRPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLRISRVEAEDLGIYYCFQGSHVPYTFGGGTKLEIKR", "cdrh1_seq": "GYTFTDYE", "cdrh2_seq": "IVPKTGYT", "cdrh3_seq": "TRLRNYWYFDV", "cdrl1_seq": "QSIVYSDGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQGSHVPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "6cdm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "vFP1.01", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp41, Human immunodeficiency virus 1", "target_domain": "Fusion peptide", "functional_role": "neutralizing", "evidence_quote": "vaccine-elicited antibody vFP1.01 neutralizes diverse strains of HIV-1"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 15691, 5113, 18, 3287, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 25618, 1927, 2616, 13141, 3413, 21, 18, 1920, 11262, 11424, 4882, 16954, 1977, 12712, 2169, 10246, 1942, 5074, 16102, 1930, 25618, 16, 2154, 8265, 4324, 6904, 2596, 4095, 1930, 30435, 2684, 2743, 1930, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 5955, 17, 9856, 12130, 3533, 5133, 1920, 5289, 4207, 16, 43, 5305, 10095, 3031, 1988, 10412, 4324, 11781, 2596, 3527, 1922, 1920, 56, 17, 4262, 5289, 4207, 4248, 18, 3], "antigen": ["AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A murine Fab, RU5 (IGHV2/IGKV10-Kappa), targeting the von Willebrand factor of Homo sapiens. Von Willebrand factor promotes adhesion of platelets to sites of vascular injury by forming a molecular bridge between sub-endothelial collagen matrix and platelet-surface receptor complex GPIb-IX-V, and acts as a chaperone for coagulation factor VIII. The antibody is designed to inhibit collagen binding, engaging the VWFA 3 domain.", "target_protein": "DVKLVQSGPGLVAPSQSLSITCTVSVSWVRQPPGKGLEWLGVTYHSALISRLSISKDNSRSQVFLKLNSLHTDDTATYYCWGQGTSVTVSSAGFSLTTYGIWGDGNTAGNYYGMDY", "metadata": {"pdb_id": "1fe8", "light_chain_seq": "DIAMTQTTSSLSASLGQKVTISCRASQDIGNYLNWYQQKPDGTVRLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLESEDIATYFCQNGGTNPWTFGGGTKLEVKRA", "cdrh1_seq": "GFSLTTYG", "cdrh2_seq": "IWGDGNT", "cdrh3_seq": "AGNYYGMDY", "cdrl1_seq": "QDIGNY", "cdrl2_seq": "YTS", "cdrl3_seq": "QNGGTNPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 103]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "1fe8", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "RU5", "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGKV10", "is_engineered": false, "target_antigen": "von Willebrand factor, Homo sapiens", "target_domain": "VWFA 3; main binding site for collagens type I and III", "functional_role": "other", "evidence_quote": "inhibits collagen binding"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 7135, 6914, 16, 7212, 1015, 12, 20733, 15755, 19, 7021, 1040, 7390, 1008, 17, 12093, 13, 16, 5133, 1920, 14147, 30067, 2991, 1927, 16350, 27974, 18, 14147, 30067, 2991, 7383, 6141, 1927, 10097, 1942, 3402, 1927, 4541, 4047, 2007, 7402, 43, 3272, 11925, 2192, 2316, 17, 5003, 5621, 4526, 1930, 7163, 17, 3154, 3148, 2796, 17497, 1014, 17, 13848, 17, 64, 16, 1930, 8016, 1966, 43, 14044, 1958, 12441, 2991, 18675, 18, 1920, 3533, 1977, 4609, 1942, 2875, 5621, 2743, 16, 15888, 1920, 17319, 1019, 23, 3418, 18, 3], "antigen": ["PDCSQPLDVILLLDGSSSFPASYFDEKSFAKAFISKANIGPRLTQVSVLQYGSITTIDVPWNVVPEKAHLLSLVDVQREGGPSQIGDALGFAVRYLTSEHGARPGASKAVVILVTDVSVDSVDAAADAARSNRVTVFPIGIGDRYDAAQLRILAGPAGDSNVVKLQRIEDLPTVTLGNSFLHKLCS"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A murine Fab, pertuzumab (IGHV3/IGKV1-Kappa), targeting the Receptor protein-tyrosine kinase erbB-2 of Homo sapiens. ErbB-2 is a protein tyrosine kinase that functions as an essential component of neuregulin-receptor complexes and regulates cell surface receptor signaling and transcriptional regulation. The antibody is designed to block ErbB2-mediated receptor dimerization and signaling by sterically occluding the dimerization interface. What would the HCDRs be?", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASMDWVRQAPGKGLEWVADIYNQRFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTFTDYTVNPNSGGSARNLGPSFYFDY", "metadata": {"pdb_id": "1s78", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCKASQDVSIGVAWYQQKPGKAPKLLIYSASYRYTGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYYIYPYTFGQGTKVEIKRT", "cdrh1_seq": "GFTFTDYT", "cdrh2_seq": "VNPNSGGS", "cdrh3_seq": "ARNLGPSFYFDY", "cdrl1_seq": "QDVSIG", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYYIYPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "1s78", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "pertuzumab", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Receptor protein-tyrosine kinase erbB-2, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "sterically blocking a binding pocket necessary for receptor dimerization and signaling"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 7135, 6914, 16, 7548, 13535, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 3148, 2213, 17, 6941, 4016, 11954, 17, 22, 1927, 16350, 27974, 18, 11954, 17, 22, 1977, 43, 2213, 6941, 4016, 1988, 4088, 1966, 1925, 4415, 4594, 1927, 2974, 6541, 3392, 17, 3148, 5048, 1930, 7014, 2024, 3154, 3148, 3197, 1930, 5224, 3640, 18, 1920, 3533, 1977, 4609, 1942, 3367, 17291, 17, 3434, 3148, 13640, 1930, 3197, 2007, 17638, 2169, 26721, 1029, 1920, 13640, 6854, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLSPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVAR"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human Fab, 1E11 (IGHV4/IGKV2-Kappa), targeting the Hemagglutinin of Influenza A virus (H7N9). Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for membrane fusion during infection. The antibody is designed as a broadly neutralizing antibody targeting the conserved stem epitope, capable of neutralizing both group 1 and group 2 influenza strains despite the divergent glycosylation patterns between HA groups. Generate the corresponding HCDRs.", "target_protein": "QVQLQESGPGLVKPSETLSLTCTVSWSWIRQPAGKALEWIGRKSNPSLESRVTMSLDASKDQFSLKLTSVTAADTAVYYCWGQGALVTVSSAGASVSSYFIYTSGNTAAGRLDYSDTTGYYKPPPLDY", "metadata": {"pdb_id": "8t1g", "light_chain_seq": "DVVMTQSPLSLPVTLGQPASISCRSSQGLAFLDGNTYLSWFQQRPGQSPRRLIYKVSNRDSGVPDRFSGSGSRTDFTLKISRVEAEDVGVYYCMQGTHWPLTFGGGTKVEIKRT", "cdrh1_seq": "GASVSSYF", "cdrh2_seq": "IYTSGNT", "cdrh3_seq": "AAGRLDYSDTTGYYKPPPLDY", "cdrl1_seq": "QGLAFLDGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "MQGTHWPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 115]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "8t1g", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "1E11", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralized across a broad panel of both group 1 and group 2 influenza strains"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 6914, 16, 10720, 3242, 12, 20733, 1020, 1006, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 12, 16754, 28955, 13, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 3260, 5289, 2409, 2909, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 5305, 4402, 10095, 16, 7131, 1927, 12130, 2321, 2210, 21, 1930, 2210, 22, 7108, 4046, 4281, 1920, 13609, 12082, 4147, 2192, 2118, 2671, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["LFGAIAGFIENGWEGLIDGWYGFRHQNAQGEGTAADYKSTQSAIDQITGKLNRLIEKTNQQFELIDNEFNEVEKQIGNVINWTRDSITEVWSYNAELLVAMENQHTIDLADSEMDKLYERVKRQLRENAEEDGTGCFEIFHKCDDDCMASIRNNTYDHSKYREEAMQNRIQIDGSGYIPEAPRDGQAYVRKDGEWVLLSTFLSGRLV", "DKICLGHHAVSNGTKVNTLTERGVEVVNATETVERTNIPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKEAMGFTYSGIRTNGATSACRRSGSSFYAEMKWLLSNTDNAAFPQMTKSYKNTRKSPALIVWGIHHSVSTAEQTKLYGSGNKLVTVGSSNYQQSFVPSPGARPQVNGLSGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGIQSGVQVDANCEGDCYHSGGTIISNLPFQNIDSRAVGKCPRYVKQRSLLLATGMKNVPEIPK"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A human Fab, CIS42 (IGHV7/IGLV2-Lambda), targeting a peptide epitope (pfCSP peptide 25: ASN-VAL-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-ASN) derived from the Circumsporozoite protein of Plasmodium falciparum. The Circumsporozoite protein is an essential sporozoite protein required for sporozoite migration through the host dermis and infection of host hepatocytes, binding to highly sulfated heparan sulfate proteoglycans on hepatocyte surfaces. This antibody forms a complex with the pfCSP peptide epitope.", "target_protein": "VQLVQSGSELKKPGASVKVSCKTSMNWVRQAPGQGLEWMGWTYAPGFTGRFVFSFDTSVSTAYLQISSLKAEDTAVYYCWGQGTLVTVSSAGYTFTTYAINTNTGNPARVYSYGVPFDY", "metadata": {"pdb_id": "6b5s", "light_chain_seq": "SVLTQPASVSGSPGQSITISCTATSSNVGSFNLVSWYQHHPGKAPKLIIHEVSKRPSGASNRFSGSKSGNTASLTISGLQAEDEADYYCCSYVGSDTWVFGGGTKLTVLGQ", "cdrh1_seq": "GYTFTTYA", "cdrh2_seq": "INTNTGNP", "cdrh3_seq": "ARVYSYGVPFDY", "cdrl1_seq": "SSNVGSFNL", "cdrl2_seq": "EVS", "cdrl3_seq": "CSYVGSDTWV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 106]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "6b5r", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CIS42", "antibody_format": "Fab", "heavy_subclass": "IGHV7", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Circumsporozoite protein, Plasmodium falciparum", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 5848, 6852, 12, 20733, 1020, 1027, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 43, 4207, 10095, 12, 14425, 3508, 4207, 2637, 30, 15118, 17, 2326, 17, 4138, 17, 1965, 17, 15118, 17, 10527, 17, 15118, 17, 1965, 17, 15118, 17, 2326, 17, 4138, 17, 1965, 17, 15118, 13, 3595, 2037, 1920, 28868, 2074, 26553, 2213, 1927, 15663, 13098, 18, 1920, 28868, 2074, 26553, 2213, 1977, 1925, 4415, 9130, 26553, 2213, 3414, 1958, 9130, 26553, 5049, 2596, 1920, 4423, 20201, 1930, 2909, 1927, 4423, 9919, 16, 2743, 1942, 3626, 26649, 22024, 8767, 25185, 1990, 14675, 7553, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 14425, 3508, 4207, 10095, 18, 3], "antigen": ["NVDPNANPNVDPN"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab, E7 (IGHV4/IGKV2-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the host cell membrane by interacting with the ACE2 receptor, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a broadly neutralizing antibody capable of neutralizing diverse SARS-CoV-2 variants and cross-clade ACE2-dependent sarbecoviruses, binding within the Receptor-binding domain (RBD).", "target_protein": "QVQLQESGPGLVKPSETLSLTCTVSWSWVRQPPGKGLEWIGYNYNPSLKSRLTISVDMSKSQFSLTLSSATAADTAVYYCWGQGTLVTVSSAGGFIGPHYIYISGSTARGGGYLETGPFEY", "metadata": {"pdb_id": "7y71", "light_chain_seq": "DIVMTQSPLSLPVTPGEPASISCRSSQSLLQNNGYNYLAWYLQKPGQSPQLLIYLSSTRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQSLQIPGTFGQGTRLEIKRT", "cdrh1_seq": "GGFIGPHY", "cdrh2_seq": "IYISGST", "cdrh3_seq": "ARGGGYLETGPFEY", "cdrl1_seq": "QSLLQNNGYNY", "cdrl2_seq": "LSS", "cdrl3_seq": "MQSLQIPGT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 108]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "7y72", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "E7", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "potent, broad-spectrum human monoclonal antibody capable of neutralizing all ACE2-binding sarbecoviruses"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 16325, 12, 20733, 1020, 1006, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 1920, 8298, 1028, 3148, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 7131, 1927, 12130, 6445, 20466, 17, 6083, 17, 22, 4936, 1930, 3567, 17, 11315, 8298, 1028, 17, 3100, 9851, 12409, 18368, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 3], "antigen": ["PAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHFDNPVLPFNDGVYFASTNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGEFRVYSSANNCTFEYVSQPFLKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNNCYFPLQSYGFQPTVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD", "PAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHDNPVLPFNDGVYFASTNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFFRVYSSANNCTFEYVSQPFLKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICAVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A murine Fab, Ky15.10-Y100EK (IGHV3/IGKV1-Kappa), targeting the Circumsporozoite protein of Plasmodium falciparum (isolate NF54). The Circumsporozoite protein is an essential sporozoite protein required for sporozoite migration through the host dermis and infection of host hepatocytes, binding to highly sulfated heparan sulfate proteoglycans on hepatocyte surfaces. The antibody is designed as a neutralizing antibody targeting the KQPA junctional peptide epitope, with the objective of achieving high-affinity cross-reactive binding to multiple PfCSP repeat motifs to confer potent sporozoite inhibition and protection against parasite liver invasion.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQVPGKGLEWVAIYYADSVKGRFSVSRDNSENTLYLQMSNLRAEDTAVYYCWGQGTTVTVSSAGFTFSNSGIWYDGSNKVRAYFDSENLYDKYGMDV", "metadata": {"pdb_id": "8fb8", "light_chain_seq": "DIQMTQSPSTLSASVGDRVTITCRASQSISRWLAWFQKKPGKAPKLLIYTASNLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYYNYWTFGQGTKVEVKRT", "cdrh1_seq": "GFTFSNSG", "cdrh2_seq": "IWYDGSNK", "cdrh3_seq": "VRAYFDSENLYDKYGMDV", "cdrl1_seq": "QSISRW", "cdrl2_seq": "TAS", "cdrl3_seq": "QQYYNYWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "8fa6", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Circumsporozoite protein, Plasmodium falciparum (isolate NF54)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "effectively inhibited Pf sporozoite traversal in vitro and reduced parasite liver load"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 7135, 6914, 16, 13995, 3962, 18, 2119, 17, 25060, 2283, 2819, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 28868, 2074, 26553, 2213, 1927, 15663, 13098, 12, 9158, 4651, 5651, 13, 18, 1920, 28868, 2074, 26553, 2213, 1977, 1925, 4415, 9130, 26553, 2213, 3414, 1958, 9130, 26553, 5049, 2596, 1920, 4423, 20201, 1930, 2909, 1927, 4423, 9919, 16, 2743, 1942, 3626, 26649, 22024, 8767, 25185, 1990, 14675, 7553, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 53, 1055, 4302, 21226, 4207, 10095, 16, 1956, 1920, 4470, 1927, 11058, 2149, 17, 5173, 3567, 17, 6079, 2743, 1942, 3137, 14425, 3508, 6865, 8277, 1942, 7909, 6828, 9130, 26553, 3523, 1930, 6202, 3316, 8652, 3568, 6254, 18, 3], "antigen": ["PDPNANPN"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A human Fab, VRC42.04 (IGHV1/IGKV3-Kappa), targeting the Envelope glycoprotein gp41 of Human immunodeficiency virus 1, specifically the RV217 founder virus gp41 peptide. The gp41 envelope glycoprotein mediates fusion of viral and host cell membranes during entry. The antibody is designed as a neutralizing antibody targeting the membrane-proximal external region (MPER), a conserved epitope class.", "target_protein": "RVQLVQSGAEVKKPGSSVRISCKASLTWVRQAPGQGLEWMGGNYTQKFQGRLTITADTSTSTSYLELSSLRSEDTAVYFCWGQGTMVVVSSAGGTFSTLTIIPLLSLPAREASGWFDKPLGAMGV", "metadata": {"pdb_id": "6mtp", "light_chain_seq": "EIVLTQSPDTLSLSPGERATLSCRASETIRNNNLAWYQQSPGQAPRLLVYGASSTATGVPGRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYYKPPGTFGQGTKVEFKRT", "cdrh1_seq": "GGTFSTLT", "cdrh2_seq": "IIPLLSLP", "cdrh3_seq": "AREASGWFDKPLGAMGV", "cdrl1_seq": "ETIRNNN", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYYKPPGT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "6mto", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "VRC42.04", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp41, Human immunodeficiency virus 1", "target_domain": "Membrane-proximal external region (MPER)", "functional_role": "neutralizing", "evidence_quote": "VRC42.04 neutralized founder virus and multiple heterologous viruses; broadly neutralizing antibody"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 2616, 6914, 16, 12110, 17875, 1028, 18, 5228, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 25618, 1927, 2616, 13141, 3413, 21, 16, 4475, 1920, 8309, 4716, 1027, 21350, 3413, 25618, 4207, 18, 1920, 25618, 11262, 11424, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 16, 43, 5305, 10095, 2921, 18, 3], "antigen": ["ASLWNWFDITKWLWYIKK"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A murine Fab, vFP16.02 (IGHV1/IGKV1-Kappa), targeting the Fusion peptide of Human immunodeficiency virus 1. The Fusion peptide is part of the Envelope glycoprotein gp160, which oligomerizes into trimers and is proteolytically cleaved to produce gp120 and gp41, initiating viral entry. The antibody is designed as a vaccine-elicited neutralizing antibody targeting the Fusion peptide, with the objective of achieving broad neutralization across diverse HIV-1 strains.", "target_protein": "QVQLLQSGAELVRPGASVTLSCKASIHWVKQTPVRGLDWIGAASNQKVKGRAILTADKSSSTAYMELRSLTSEDSAVYYCWGTGTTVTVSSAGYAFSDYEFDPKSGASTRLRYFGYFDV", "metadata": {"pdb_id": "6wx2", "light_chain_seq": "DVLMTQTPLSLPVSLGGQASISCRSSQSVVYSDGDTYLEWYLQKPGQSPKLLIYKVSRRPSGVPDRFSGSGSGTDFTLKISRVETEDLGVYYCFQGSHVPYTFGGGTKLEIKRT", "cdrh1_seq": "GYAFSDYE", "cdrh2_seq": "FDPKSGAS", "cdrh3_seq": "TRLRYFGYFDV", "cdrl1_seq": "QSVVYSDGDTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQGSHVPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "6wx2", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "vFP16.02", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Fusion peptide, Human immunodeficiency virus 1", "target_domain": "Fusion peptide", "functional_role": "neutralizing", "evidence_quote": "vaccine-elicited anti-FP antibody...neutralization breadth"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 7135, 6914, 16, 15691, 5113, 1016, 18, 5725, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 5289, 4207, 1927, 2616, 13141, 3413, 21, 18, 1920, 5289, 4207, 1977, 3131, 1927, 1920, 11262, 11424, 4882, 16954, 16, 2154, 13034, 4517, 2460, 28220, 1930, 1977, 12712, 2169, 10246, 1942, 5074, 16102, 1930, 25618, 16, 12410, 4324, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 5955, 17, 9856, 12130, 3533, 5133, 1920, 5289, 4207, 16, 1956, 1920, 4470, 1927, 11058, 4949, 14377, 3436, 6445, 3525, 17, 21, 4046, 18, 3], "antigen": ["AVGIGAVF"]} {"modality_type": "antibody", "text": "Output the HCDRs for an antibody that performs this function: A human Fab, 31.a.83 (IGHV3/IGKV3-Kappa), targeting the engineered Hemagglutinin of Influenza A virus (A/Hong Kong/1-4-MA21-1/1968(H3N2)). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and serves as a class I viral fusion protein responsible for penetration into the cell cytoplasm. The antibody is designed as a broadly neutralizing antibody targeting the conserved HA stem, capable of neutralizing both group 1 and group 2 influenza A subtypes while avoiding conserved glycan shields.", "target_protein": "VQLLESGGGLVQPGESLRVSCAASLSWVRQAPGKGLEWVSAYYADTVKGRFTISRDNSQTTLYLQMNSLRADDTATYYCWGKGTTVTVSSSGFTFRDSAISGNGGATAKDESPPIYNLMPGYYSTYYYMDV", "metadata": {"pdb_id": "5kaq", "light_chain_seq": "EIVMTQSPVTLSVSPGETATLSCRASQSVRSNLAWYQQKPGQAPRLLIYGASTRATDIPARFSGSGSGTEFTLSISSLQSDDFAVYYCQQYNHWLRTFGQGTKLEIKTV", "cdrh1_seq": "GFTFRDSA", "cdrh2_seq": "ISGNGGAT", "cdrh3_seq": "AKDESPPIYNLMPGYYSTYYYMDV", "cdrl1_seq": "QSVRSN", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYNHWLRT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 118]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5kaq", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "31.a.83", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus (A/Hong Kong/1-4-MA21-1/1968(H3N2))", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing all of the common influenza A subtypes that infect humans"}}}, "tokenized_instruction": [2, 6647, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 17436, 2052, 2347, 30, 43, 2616, 6914, 16, 3470, 18, 43, 18, 5893, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 26141, 1927, 7108, 43, 3413, 12, 43, 19, 15908, 18143, 19, 21, 17, 24, 17, 2488, 4716, 17, 21, 19, 22553, 12, 25234, 13, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 10634, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 12006, 2460, 1920, 2024, 5239, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 5305, 2118, 4402, 16, 7131, 1927, 12130, 2321, 2210, 21, 1930, 2210, 22, 7108, 43, 8160, 2679, 13910, 5305, 15060, 19397, 1036, 18, 3], "antigen": ["ATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIESRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQ"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human Fab, 5-24 (IGHV3/IGKV3-Kappa), targeting the engineered prefusion Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the host cell membrane by interacting with ACE2 and other receptors, and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting the NTD supersite, a glycan-free, electropositive surface comprising flexible loops and the N3 \u03b2-hairpin that faces away from the viral membrane. Please generate the HCDRs for this antibody.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLDWVGVYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTTVTGLTFSSYVIWYDGSKKARDPRDYYDFWSGYDYYYGLDV", "metadata": {"pdb_id": "7l2f", "light_chain_seq": "EIVLTQSPGILSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSGALTFGGGTKVEIK", "cdrh1_seq": "GLTFSSYV", "cdrh2_seq": "IWYDGSKK", "cdrh3_seq": "ARDPRDYYDFWSGYDYYYGLDV", "cdrl1_seq": "QSVSSSY", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYGSSGALT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 117]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "7l2f", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "5-24", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "N-terminal domain (NTD)", "functional_role": "neutralizing", "evidence_quote": "NTD-directed neutralizing antibody 5-24 in complex with prefusion SARS-CoV-2 spike"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 25, 17, 2686, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 9328, 2670, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 8298, 1028, 1930, 2303, 4086, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 22078, 12636, 2394, 16, 43, 15060, 17, 3294, 16, 4260, 2420, 2470, 3154, 10351, 9964, 11109, 1930, 1920, 18971, 161, 17, 14565, 1988, 11135, 8952, 2037, 1920, 4324, 3260, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A human Fab, DL11 (IGHV3/IGKV1-Kappa), targeting the engineered Epidermal growth factor receptor of Homo sapiens. The Epidermal growth factor receptor is a receptor tyrosine kinase that binds ligands of the EGF family and activates multiple downstream signaling cascades including RAS-RAF-MEK-ERK, PI3 kinase-AKT, PLCgamma-PKC, and STATs pathways. The antibody is designed to inhibit EGFR-mediated signaling as part of a dual-specificity approach targeting both EGFR and HER3. Please provide the HCDR sequences.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWLGEDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTLSGDWISAAGGYTARESRVSFEAAMDY", "metadata": {"pdb_id": "3p0y", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQDLATDVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSEPEPYTFGQGTKVEIKRT", "cdrh1_seq": "GFTLSGDW", "cdrh2_seq": "ISAAGGYT", "cdrh3_seq": "ARESRVSFEAAMDY", "cdrl1_seq": "QDLATD", "cdrl2_seq": "SAS", "cdrl3_seq": "QQSEPEPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3p11", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DL11", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Epidermal growth factor receptor, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "inhibiting EGFR- and HER3-mediated signaling in vitro and in vivo"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 2616, 6914, 16, 5268, 3242, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 9844, 2905, 2991, 3148, 1927, 16350, 27974, 18, 1920, 9844, 2905, 2991, 3148, 1977, 43, 3148, 6941, 4016, 1988, 6876, 6908, 1927, 1920, 4451, 3416, 1930, 9094, 3137, 5863, 3197, 15967, 2710, 6520, 17, 12783, 17, 12551, 17, 7770, 16, 21197, 4016, 17, 5496, 16, 12897, 4223, 28262, 17, 8425, 16, 1930, 3156, 1036, 3873, 18, 1920, 3533, 1977, 4609, 1942, 2875, 5775, 17, 3434, 3197, 1966, 3131, 1927, 43, 7064, 17, 4896, 2998, 5133, 2321, 5775, 1930, 3656, 1010, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["RKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCR"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A murine Fab, OXI-005 (IGHV5/IGKV19-Kappa), targeting porcine Insulin. Insulin decreases blood glucose concentration by increasing cell permeability to monosaccharides, amino acids and fatty acids, and accelerating glycolysis, the pentose phosphate cycle, and glycogen synthesis in liver. This analytical antibody forms a complex with the dimeric Insulin. Please output the HCDRs.", "target_protein": "EVQLVESGGGLVKPGGSLKLSCTASMSWVRQTPEKRLEWVAFYYPDTVKGRFTISRDNAENTLYLQMSSLKSEDTAIYYCWGLGTTLTVSSAGFAFSDYDISNGGYSTARQGLRYFDY", "metadata": {"pdb_id": "6z7z", "light_chain_seq": "DIQMTQSPSSLSASLGGRVTITCKASQDINKYLAWYQHKPGKGPRLLIHYTSTLQPGIPSRFSGSGSGRDYSFSISNLEPEDVATYYCLQYDSLLSFGAGTKLELKRA", "cdrh1_seq": "GFAFSDYD", "cdrh2_seq": "ISNGGYST", "cdrh3_seq": "ARQGLRYFDY", "cdrl1_seq": "QDINKY", "cdrl2_seq": "YTS", "cdrl3_seq": "LQYDSLLS", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 105]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6z7z", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "OXI-005", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV19", "is_engineered": false, "target_antigen": "Insulin, Sus scrofa", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 2833, 1033, 17, 9163, 12, 20733, 1020, 1015, 19, 7021, 1040, 7390, 1026, 17, 12093, 13, 16, 5133, 12966, 4122, 18, 4122, 6386, 2877, 3817, 3110, 2007, 3605, 2024, 8828, 1942, 18491, 11926, 16, 3835, 4576, 1930, 5934, 4576, 16, 1930, 21436, 13393, 16, 1920, 9412, 2217, 5413, 4048, 16, 1930, 13302, 4271, 1922, 3568, 18, 2052, 8657, 3533, 4952, 43, 2796, 1956, 1920, 18150, 4122, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["NQHLCGSHLVEALYLVCGERGFFYTPKA", "GIVEQCCTSICSLYQLENYCN"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A murine Fab, D12 (IGHV5/IGKV10-Kappa), targeting the Spike glycoprotein of Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host DPP4 receptor and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a vaccine-elicited neutralizing antibody, binding within the BetaCoV S1-CTD. Generate the corresponding HCDRs.", "target_protein": "EVKLVESGGGLVKPGGSLKLSCAASMSWVRQTPEKRLEWVATYYPDSVKGRFTISRDNAENTLYLQMSSLRSEDTAMYYCWGQGTSVTVSSAGFTFSSYAISSGGTYTVRDGNSMDY", "metadata": {"pdb_id": "4zpt", "light_chain_seq": "DIQMTQTTSSLSASLGDRVTIICRASQDINNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGSDYSLTISNLEQEDIATYFCQQANTLPPTFGAGTKLELRRA", "cdrh1_seq": "GFTFSSYA", "cdrh2_seq": "ISSGGTYT", "cdrh3_seq": "VRDGNSMDY", "cdrl1_seq": "QDINNY", "cdrl2_seq": "YTS", "cdrl3_seq": "QQANTLPPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 104]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "4zpt", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "D12", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV10", "is_engineered": false, "target_antigen": "Spike glycoprotein, Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)", "target_domain": "BetaCoV S1-CTD", "functional_role": "neutralizing", "evidence_quote": "vaccine-elicited murine neutralizing antibody; immunization elicits NAbs to RBD"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 8524, 1028, 12, 20733, 1020, 1015, 19, 7021, 1040, 7390, 1008, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 5576, 10319, 5481, 4741, 17, 2712, 5548, 10703, 12, 9158, 6128, 13543, 19, 21907, 6021, 5124, 23959, 19, 3775, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 16423, 1006, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 5955, 17, 9856, 12130, 3533, 16, 2743, 2651, 1920, 4666, 4879, 1020, 4062, 17, 15898, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKL"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab (IGHV3/IGLV1-Lambda) targeting the engineered prefusion Fusion glycoprotein F0 of Respiratory syncytial virus A2. The Fusion glycoprotein F0 is a class I viral fusion protein that mediates fusion of viral and cellular membranes during entry. This antibody is one of three MxR Fabs in the complex and is designed as a cross-neutralizing antibody against RSV and human metapneumovirus, binding to antigenic site III.", "target_protein": "EVQVVESGGGLVKPGGSLRLSCAASMDWVRQAPGKGLEWVSSNYADSVKGRFTISRDNAKNSLYLQMKSLRADDTAVYFCWGQGILVTVSSGFPFSSYKISASGSYIARDGGRELSPFEK", "metadata": {"pdb_id": "8dg9", "light_chain_seq": "QSVLTQPPSVSGAPGQRVTISCTGTNSNIGTGYDVHWYQQLPGTAPKVVLFDNNNRPSGVPDRFSGSKSGTSAALAITGLQAEDEAVYYCQSYDKSLGGWVFGGGTKLTVL", "cdrh1_seq": "GFPFSSYK", "cdrh2_seq": "ISASGSYI", "cdrh3_seq": "ARDGGRELSPFEK", "cdrl1_seq": "NSNIGTGYD", "cdrl2_seq": "DNN", "cdrl3_seq": "QSYDKSLGGWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[25, 33]", "cdrl2_pos": "[51, 53]", "cdrl3_pos": "[90, 100]", "cdrh3_split": "val", "cdrh3_cluster": "8dg9", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Fusion glycoprotein F0, Respiratory syncytial virus A2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "cross-neutralizing antibodies to respiratory syncytial virus, human metapneumovirus"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 28961, 7390, 17, 18279, 13, 5133, 1920, 11091, 9328, 2670, 5289, 11424, 17930, 1927, 5481, 29988, 3413, 8595, 18, 1920, 5289, 11424, 17930, 1977, 43, 2921, 51, 4324, 5289, 2213, 1988, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2409, 6904, 18, 2052, 3533, 1977, 2340, 1927, 2559, 18595, 1005, 6914, 1036, 1922, 1920, 2796, 1930, 1977, 4609, 1966, 43, 3567, 17, 12130, 3533, 3316, 12390, 1930, 2616, 5880, 27257, 3708, 12492, 11074, 16, 2743, 1942, 14606, 3200, 4337, 18, 3], "antigen": ["QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKDAKVKLIKQELDKYKNAVTELQLLMFLGFLLGVGSAIASGVAVCKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTFKVLDLKNYIDKQLLPILCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELL"]} {"modality_type": "antibody", "text": "What would be the HCDR sequences of an antibody with the following function: A murine Fab (IGHV1/IGKV4-Kappa) targeting the Hemagglutinin of Influenza A virus (A/Solomon Islands/3/2006(H1N1)). Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and internalization, and functions as a class I viral fusion protein responsible for penetration of the virus into the cell cytoplasm. This antibody forms a complex with the Hemagglutinin.", "target_protein": "QLQQSGPELVKPGASVKISCKASMNWVKQSDGKSLEWIGISYNQKFKGKATLTVDQSSSTAYMQLNSLTSEDSAVYYCWGKGTTVTVSGYSFTDYNINPNYGIIARWGNSPYYYYYMDV", "metadata": {"pdb_id": "7umn", "light_chain_seq": "ENVLTQSPAIMSASPGEKVTMTCRATSSVSSSYLHWYQQKSGASPKLWIYGTSNLASGVPARFSGSGSGTSYSLTISTVEAEDAATYYCQQYSGYPLTFGAGTKLEL", "cdrh1_seq": "GYSFTDYN", "cdrh2_seq": "INPNYGII", "cdrh3_seq": "ARWGNSPYYYYYMDV", "cdrl1_seq": "SSVSSSY", "cdrl2_seq": "GTS", "cdrl3_seq": "QQYSGYPLT", "cdrh1_pos": "[23, 30]", "cdrh2_pos": "[48, 55]", "cdrh3_pos": "[94, 108]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "7umn", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus (A/Solomon Islands/3/2006(H1N1))", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1920, 26141, 1927, 7108, 43, 3413, 12, 43, 19, 2638, 20050, 13408, 19, 23, 19, 3956, 12, 15355, 13, 13, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 12071, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 12006, 1927, 1920, 3413, 2460, 1920, 2024, 5239, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 26141, 18, 3], "antigen": ["HNGKLCLLKGIAPLQLGNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEVLVLWGVHHPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDQEGRINYYWTLLEPGDTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSAGKEFNKLERRMENLNKKVDDGFIDIWTY"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A murine Fab (IGHV1/IGKV1-Kappa) targeting beta-theraphotoxin-Cm1a, a peptide toxin from the spider Ceratogyrus marshalli. Beta-theraphotoxin-Cm1a inhibits voltage-gated sodium channels including Nav1.7, Nav1.2, Nav1.1, Nav1.4, and Nav1.5, and the voltage-gated calcium channel Cav2.2, acting by shifting the voltage dependence of channel activation and blocking the inward sodium current. This antibody forms a complex with the beta-theraphotoxin-Cm1a toxin.", "target_protein": "VQLQQPGAELLRPGASVKLSCKASMNWVKQRPGQGLELIGMHYNQMFKDKATLTVDKSSSTAYMQLSSLTSEDSAVYYCWGQGTTVTVSSAGYTFTNFWIDPSDSETARRDYYGILFDY", "metadata": {"pdb_id": "5epm", "light_chain_seq": "DVLMTQTPLSLPVSLGDQASISCRSSQSIVHNNGNTYIEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIKRA", "cdrh1_seq": "GYTFTNFW", "cdrh2_seq": "IDPSDSET", "cdrh3_seq": "ARRDYYGILFDY", "cdrl1_seq": "QSIVHNNGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQGSHVPFT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 106]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "5epm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Beta-theraphotoxin-Cm1a, Ceratogyrus marshalli", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 4666, 17, 2709, 10647, 4575, 10960, 17, 3195, 6146, 16, 43, 4207, 9165, 2037, 1920, 26376, 6580, 8286, 26983, 3176, 1036, 20645, 2214, 1033, 18, 4666, 17, 2709, 10647, 4575, 10960, 17, 3195, 6146, 7042, 6889, 17, 12336, 5227, 5628, 2710, 18753, 18, 27, 16, 18753, 18, 22, 16, 18753, 18, 21, 16, 18753, 18, 24, 16, 1930, 18753, 18, 25, 16, 1930, 1920, 6889, 17, 12336, 5016, 4999, 9879, 1028, 18, 22, 16, 8290, 2007, 15332, 1920, 6889, 6816, 1927, 4999, 2936, 1930, 7472, 1920, 16998, 5227, 3214, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 4666, 17, 2709, 10647, 4575, 10960, 17, 3195, 6146, 9165, 18, 3], "antigen": ["DCLGMFKSCDPENDKCCKRLVCSRSHRWCKWKL"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A murine Fab (IGHV1/IGKV4-Kappa) targeting the engineered extracellular domains of human T-cell surface glycoprotein CD4. CD4 serves as the primary receptor for human immunodeficiency virus-1 and plays an essential role in immune responses through interactions with MHC class II molecules and the T-cell receptor. The antibody, ibalizumab, is designed to inhibit HIV entry by stabilizing a conformational state of CD4 that re-orients the gp120 binding site away from incoming virus, preventing productive viral attachment. What would the HCDRs be?", "target_protein": "QVQLQQSGPEVVKPGASVKMSCKASIHWVRQKPGQGLDWIGYDYDEKFKGKATLTSDTSTSTAYMELSSLRSEDTAVYYCWGQGTLVTVSSAGYTFTSYVINPYNDGTAREKDNYATGAWFAY", "metadata": {"pdb_id": "7t0r", "light_chain_seq": "DIVMTQSPDSLAVSLGERVTMNCKSSQSLLYSTNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSVQAEDVAVYYCQQYYSYRTFGGGTKLEIKRT", "cdrh1_seq": "GYTFTSYV", "cdrh2_seq": "INPYNDGT", "cdrh3_seq": "AREKDNYATGAWFAY", "cdrl1_seq": "QSLLYSTNQKNY", "cdrl2_seq": "WAS", "cdrl3_seq": "QQYYSYRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 101]", "cdrh3_split": "val", "cdrh3_cluster": "7t0r", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "T-cell surface glycoprotein CD4, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "inhibits downstream actions of gp160; prevents productive viral attachment"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1920, 11091, 5329, 4682, 1927, 2616, 62, 17, 2024, 3154, 11424, 4095, 18, 4095, 10634, 1966, 1920, 3065, 3148, 1958, 2616, 13141, 3413, 17, 21, 1930, 5705, 1925, 4415, 2770, 1922, 3743, 3387, 2596, 3719, 1956, 8709, 2921, 2890, 4206, 1930, 1920, 62, 17, 2024, 3148, 18, 1920, 3533, 16, 27931, 12191, 19240, 3368, 1014, 16, 1977, 4609, 1942, 2875, 3525, 6904, 2007, 14384, 43, 8523, 3360, 1927, 4095, 1988, 1964, 17, 5567, 1036, 1920, 16102, 2743, 3200, 8952, 2037, 22201, 3413, 16, 8444, 16343, 4324, 8576, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQKASSIVYKKEGEQVEFSFPLAFTVEKLTGSGELWWQAERASSSKSWITFDLKNKEVSVKRVTQDPKLQMGKKLPLHLTLPQALPQYAGSGNLTLALEAKTGKLHQEVNLVVMRATQLQKNLTCEVWGPTSPKLMLSLKLENKEAKVSKREKAVWVLNPEAGMWQCLLSDSGQVLLESNIKV"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A human Fab (IGHV3/IGKV1-Kappa) targeting the engineered Hepatocyte growth factor activator serine protease of Homo sapiens. The serine protease hydrolyzes the inactive zymogen hepatocyte growth factor (HGFsc) to an activated disulfide-linked heterodimer, initiating hepatocyte growth factor receptor signaling. The antibody is designed as an allosteric inhibitor that imposes a conformational change on the 99-loop to disrupt substrate binding, binding within the Peptidase S1 domain at the periphery of the substrate binding cleft.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVGGYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTINGTYIYPAGGATAKWAWPAFDY", "metadata": {"pdb_id": "2wuc", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSNRAPATFGQGTKVEIKRT", "cdrh1_seq": "GFTINGTY", "cdrh2_seq": "IYPAGGAT", "cdrh3_seq": "AKWAWPAFDY", "cdrl1_seq": "QDVSTA", "cdrl2_seq": "SAS", "cdrl3_seq": "QQSNRAPAT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 105]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "2wuc", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Hepatocyte growth factor activator serine protease, Homo sapiens", "target_domain": "Peptidase S1", "functional_role": "other", "evidence_quote": "allosteric inhibitor of HGFA catalytic activity via conformational change"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11091, 14675, 2905, 2991, 9518, 8468, 7154, 1927, 16350, 27974, 18, 1920, 8468, 7154, 7222, 20887, 1920, 9078, 15856, 2404, 14675, 2905, 2991, 12, 14757, 12709, 13, 1942, 1925, 4128, 11830, 17, 4624, 15672, 16, 12410, 14675, 2905, 2991, 3148, 3197, 18, 1920, 3533, 1977, 4609, 1966, 1925, 14772, 4106, 1988, 26926, 1036, 43, 8523, 3185, 1990, 1920, 4922, 17, 5881, 1942, 12512, 4510, 2743, 16, 2743, 2651, 1920, 24050, 4062, 3418, 2019, 1920, 13119, 1927, 1920, 4510, 2743, 14649, 18, 3], "antigen": ["IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIRP"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: Human Fab antibodies (IGHV3/IGKV3-Kappa) targeting the Hemagglutinin HA2 subunit of Influenza A virus. Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and is responsible for fusion of the viral membrane with the endosomal membrane during infection. These antibodies are designed as broadly protective neutralizing antibodies targeting conserved epitopes in the HA stem and head trimer interface to elicit universal influenza immunity across diverse viral strains. Can you generate its HCDRs?", "target_protein": "EVQLLESGGGLVQPGESLRVSCAASLSWVRQAPGKGLEWVSAYYADTVKGRFTISRDNSQTTLYLQMNSLRADDTATYYCWGKGTTVTVSSAGFTFRDSAISGNGGATAKDESPPIYNLMPGYYSTYYYMDV", "metadata": {"pdb_id": "7u8m", "light_chain_seq": "EIVMTQSPVTLSVSPGETATLSCRASQSVRSNLAWYQQKPGQAPRLLIYGASTRATDIPARFSGSGSGTEFTLSISSLQSDDFAVYYCQQYNHWLRTFGQGTKLEIRTV", "cdrh1_seq": "GFTFRDSA", "cdrh2_seq": "ISGNGGAT", "cdrh3_seq": "AKDESPPIYNLMPGYYSTYYYMDV", "cdrl1_seq": "QSVRSN", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYNHWLRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 119]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5kaq", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Hemagglutinin HA2 subunit, Influenza A virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "broadly protective antibodies targeting conserved regions of the HA unlock the possibility of generating universal influenza immunity"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 2616, 6914, 3788, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 26141, 2118, 1028, 5903, 1927, 7108, 43, 3413, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 1977, 5061, 1958, 5289, 1927, 1920, 4324, 3260, 1956, 1920, 16514, 3260, 2409, 2909, 18, 2144, 3788, 2032, 4609, 1966, 11984, 6337, 12130, 3788, 5133, 5305, 11427, 1922, 1920, 2118, 4402, 1930, 4469, 20085, 6854, 1942, 12095, 10321, 7108, 7611, 3436, 6445, 4324, 4046, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["GIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQI"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A murine Fab (IGHV5/IGKV1-Kappa), Fab4C1, targeting the Alpha-mammal toxin AaH2 of Androctonus australis hector. Alpha-mammal toxin AaH2 binds voltage-independently at site-3 of sodium channels, inhibits channel inactivation, and blocks neuronal transmission by stabilizing a deactivated state in the voltage-sensing domain. The antibody is designed as a neutralizing antibody with high affinity and selectivity for AaH2, binding within the LCN-type CS-alpha/beta domain.", "target_protein": "EVHLVESGGGLVKPGGSLKLSCAASMYWVRQTPEKRLEWVASYYPDSVKGRFTISRDNAKNNLYLQMSSLRSDDTAMYYCWGQGTLVTVSAAGFTFSGYYISDGGSFTSRPDDYSYDGFAY", "metadata": {"pdb_id": "4aei", "light_chain_seq": "DVLMTQSPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPNLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELKRA", "cdrh1_seq": "GFTFSGYY", "cdrh2_seq": "ISDGGSFT", "cdrh3_seq": "SRPDDYSYDGFAY", "cdrl1_seq": "QSIVHSNGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQGSHVPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "4aei", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Alpha-mammal toxin AaH2, Androctonus australis hector", "target_domain": "LCN-type CS-alpha/beta", "functional_role": "neutralizing", "evidence_quote": "high affinity and selectivity for AahII and efficient neutralization"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 7135, 6914, 12, 20733, 1020, 1015, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 6914, 25077, 1009, 16, 5133, 1920, 4595, 17, 28582, 9165, 6440, 6951, 1927, 1930, 4104, 5405, 1957, 9417, 1937, 28702, 2684, 18, 4595, 17, 28582, 9165, 6440, 6951, 6876, 6889, 17, 6407, 2019, 3200, 17, 23, 1927, 5227, 5628, 16, 7042, 4999, 8005, 16, 1930, 7644, 5121, 5303, 2007, 14384, 43, 30097, 2341, 17370, 2013, 3360, 1922, 1920, 6889, 17, 9306, 3418, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1956, 2149, 5173, 1930, 9008, 1958, 6440, 6951, 16, 2743, 2651, 1920, 5236, 1022, 17, 2601, 3752, 17, 4595, 19, 4666, 3418, 18, 3], "antigen": ["VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYKLPDHVRTKGPGRCH"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A human Fab (IGHV3/IGKV1-Kappa) targeting a linear epitope (residues 3\u20137) of the amyloid-beta peptide derived from the amyloid-beta precursor protein. The amyloid-beta peptide functions in metal chelation, tau aggregation, and neuronal interactions relevant to Alzheimer's disease pathology. The antibody is designed to selectively engage aggregated amyloid-beta species over monomeric forms through weak monovalent affinity and avidity-driven binding to epitope-rich oligomeric and fibrillar aggregates, with the goal of targeting pathological amyloid-beta variants while sparing non-pathogenic monomers.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVAVYYTDSVKGRFTISRDNSKNTLYLQMNTLRAEDTAVYYCWGKGTTVTVSSAGFAFSSYGIWFDGTKKARDRGIGARRGPYYMDV", "metadata": {"pdb_id": "6co3", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLTFGGGTKVEIKRT", "cdrh1_seq": "GFAFSSYG", "cdrh2_seq": "IWFDGTKK", "cdrh3_seq": "ARDRGIGARRGPYYMDV", "cdrl1_seq": "QSISSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSYSTPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6co3", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Amyloid-beta precursor protein, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "selectively targets aggregated A\u03b2 with very weak affinity for monomers and strong avidity for aggregates"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 43, 4258, 10095, 12, 4248, 23, 229, 27, 13, 1927, 1920, 8186, 17, 4666, 4207, 3595, 2037, 1920, 8186, 17, 4666, 7897, 2213, 18, 1920, 8186, 17, 4666, 4207, 4088, 1922, 6048, 28526, 16, 7462, 7883, 16, 1930, 5121, 3719, 4494, 1942, 9116, 11, 61, 2573, 6819, 18, 1920, 3533, 1977, 4609, 1942, 9331, 11580, 14686, 8186, 17, 4666, 3038, 2338, 14457, 4952, 2596, 5015, 28685, 5173, 1930, 24673, 17, 6446, 2743, 1942, 10095, 17, 5536, 19206, 1930, 24271, 9748, 16, 1956, 1920, 6640, 1927, 5133, 6598, 8186, 17, 4666, 4936, 2679, 17981, 2447, 17, 8070, 13256, 18, 3], "antigen": ["AEFRHD"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A Fab (IGHV4/IGLV1-Lambda) targeting an engineered fusion construct of the human Potassium voltage-gated channel subfamily A member 3 (Kv1.3) with Green fluorescent protein (N- to C-terminus). Kv1.3 mediates voltage-dependent potassium ion permeability of excitable membranes by forming a potassium-selective channel. This Fab is fused to the ShK toxin to create a monovalent Fab-ShK inhibitor that blocks Kv1.3 currents by positioning the toxin at the channel pore mouth, serving as a structural tool for cryo-EM characterization of channel modulation.", "target_protein": "QVQLREWGAGLLKPSETLSLTCAVYWSWIRQPPGKGLEWIGSNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCWGQGLLVTVSSAGGSFSDKYINHSGSTTSVHQETKRSCIDTIPKSRCTAFQCKHSMKYRLSFCRKTCGTCNYEWHVDV", "metadata": {"pdb_id": "7ssv", "light_chain_seq": "LNQPSSVSGSLGQKVTISCSGSSSNIGNNYVSWYQQLPGTAPKLLIYGDTKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCASAEDSSSNAVFGSGTTLTVLGQ", "cdrh1_seq": "GGSFSDKY", "cdrh2_seq": "INHSGST", "cdrh3_seq": "TSVHQETKRSCIDTIPKSRCTAFQCKHSMKYRLSFCRKTCGTCNYEWHVDV", "cdrl1_seq": "SSNIGNNY", "cdrl2_seq": "GDT", "cdrl3_seq": "ASAEDSSSNAV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 145]", "cdrl1_pos": "[22, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7ssv", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Potassium voltage-gated channel subfamily A member 3 fused to Green fluorescent protein, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "Fab-ShK can bind only one Kv1.3 channel, thereby forming a protein complex amenable to single particle cryo-EM structure determination"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 6914, 12, 20733, 1020, 1006, 19, 28961, 7390, 17, 18279, 13, 5133, 1925, 11091, 5289, 6377, 1927, 1920, 2616, 9057, 6889, 17, 12336, 4999, 16227, 43, 7210, 23, 12, 23397, 18, 23, 13, 1956, 4524, 6265, 2213, 12, 56, 17, 1942, 45, 17, 7822, 13, 18, 23397, 18, 23, 10412, 6889, 17, 3100, 9057, 4755, 8828, 1927, 7817, 2115, 5726, 2007, 7402, 43, 9057, 17, 5328, 4999, 18, 2052, 6914, 1977, 10305, 1942, 1920, 2044, 1040, 9165, 1942, 7762, 43, 28685, 6914, 17, 2044, 1040, 4106, 1988, 7644, 23397, 18, 23, 9058, 2007, 12158, 1920, 9165, 2019, 1920, 4999, 8554, 11701, 16, 13915, 1966, 43, 4346, 5229, 1958, 15822, 17, 2391, 7285, 1927, 4999, 7145, 18, 3], "antigen": ["GERVVINISGLRFETQLKTLCQFPETLLGDPKRRMRYFDPLRNEYFFDRNRPSFDAILYYYQSGGRIRRPVNVPIDIFSEEIRFYQLGEEAMEKFREDEGFLREEERPLPRRDFQRQVWLLFEYPESSGPARGIAIVSVLVILISIVIFCLETLPEFSSFSDPFFVVETLCIIWFSFELLVRFFACPSKATFSRNIMNLIDIVAIIPYFITLGTELASLAILRVIRLVRVFRIFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGVILFSSAVYFAEADDPTSGFSSIPDAFWWAVVTMTTVGYGDMHPVTIGGKIVGSLCAIAGVLTIALPVPVIVSNFNYFYHRET"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: Human Fab antibodies (IGHV1/IGKV1-Kappa) targeting the Spike protein S1 of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors, initiating infection and mediating fusion of viral and cellular membranes. These antibodies are designed as neutralizing antibodies targeting the Receptor-binding domain (RBD), with the objective of blocking viral entry and preventing membrane fusion. Can you generate its HCDRs?", "target_protein": "QVQLVQSGAEVKKPGSSVKVSCKASISWVRQAPGQGLEWMGGNYAQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCWGQGTLVTVSSAGYTFTSYGIIPMFGTTARDRGDTIDY", "metadata": {"pdb_id": "7k9z", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQGISNNLNWYQQKPGKAPKLLIYAASSLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQGNGFPLTFGPGTKVDIKRT", "cdrh1_seq": "GYTFTSYG", "cdrh2_seq": "IIPMFGTT", "cdrh3_seq": "ARDRGDTIDY", "cdrl1_seq": "QGISNN", "cdrl2_seq": "AAS", "cdrl3_seq": "QQGNGFPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 105]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7k9z", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Spike protein S1, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibodies targeting the SARS-CoV-2 S glycoprotein"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 2616, 6914, 3788, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 10429, 2213, 4062, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 16, 12410, 2909, 1930, 10239, 5289, 1927, 4324, 1930, 3689, 5726, 18, 2144, 3788, 2032, 4609, 1966, 12130, 3788, 5133, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 1956, 1920, 4470, 1927, 7472, 4324, 6904, 1930, 8444, 3260, 5289, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A murine Fab, 9F8 (IGHV2/IGKV6-Kappa), targeting the Leptin receptor of Homo sapiens. The Leptin receptor mediates leptin's central and peripheral effects through activation of signaling pathways including JAK2/STAT3 and MAPK cascade, regulating energy homeostasis, fertility, and immune function. The antibody is designed to block leptin binding to the receptor, antagonizing leptin signaling. What would the HCDRs be?", "target_protein": "EVKLLESGPGLVAPSESLSITCTISVSWIRQPPGKGLEWLGVYFNSLFKSRLSITRDNSKSQVFLEMDSLQTDDTAMYYCWGQGTSVTVSSSGFSLTDDGIWGGGSTAKHDGHETMDY", "metadata": {"pdb_id": "3v6o", "light_chain_seq": "IVMTQSPKFMSTSIGDRVNITCKATQNVRTAVTWYQQKPGQSPQALIFLASNRHTGVPARFTGSGSGTDFTLTINNVKSEDLADYFCLQHWNYPLTFGSGTKLEIKRA", "cdrh1_seq": "GFSLTDDG", "cdrh2_seq": "IWGGGST", "cdrh3_seq": "AKHDGHETMDY", "cdrl1_seq": "QNVRTA", "cdrl2_seq": "LAS", "cdrl3_seq": "LQHWNYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 105]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "3v6o", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "9F8", "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGKV6", "is_engineered": false, "target_antigen": "Leptin receptor, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "leptin-blocking monoclonal antibody"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 7135, 6914, 16, 29, 1038, 1025, 12, 20733, 15755, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 9598, 3148, 1927, 16350, 27974, 18, 1920, 9598, 3148, 10412, 9598, 11, 61, 4101, 1930, 5009, 2564, 2596, 2936, 1927, 3197, 3873, 2710, 15474, 19, 8919, 1930, 7859, 9861, 16, 6773, 3844, 7622, 16, 11869, 16, 1930, 3743, 2347, 18, 1920, 3533, 1977, 4609, 1942, 3367, 9598, 2743, 1942, 1920, 3148, 16, 5605, 3903, 9598, 3197, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["NINISCETDGYLTKMTCRWSTSTLQLRYHRSSLYCSDIPSIHPISEPKDCYLQSDGFYECIFQPIFLLSGYTMWIRINGSLDSPPTCVLPDSVVKPLPPSSVKAEITINIGLLKISWNLQFQIRYGLSGKEVQWKMYEVYDKSVSLPVPDLCAVYAVQVRCKRLDGLGYWSNWSNPAYTVV"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A human Fab, 14N4 (IGHV3/IGKV1-Kappa), targeting the engineered postfusion Fusion glycoprotein F0 of Human respiratory syncytial virus A. The Fusion glycoprotein F0 is a class I viral fusion protein that mediates fusion of viral and cellular membranes during entry. The antibody is designed as a neutralizing antibody targeting antigenic site II, with binding geometry that avoids interference from nonneutralizing site II antibodies.", "target_protein": "VESGGGLIQPGGSLRLSCAVSMTWVRQAPGKGLEWVSVYYADSVVGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTVSSKYIYGGGSTASRLGVRATTGDLDY", "metadata": {"pdb_id": "5j3d", "light_chain_seq": "DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYNTYSWWTFGQGTKVDIKRT", "cdrh1_seq": "GFTVSSKY", "cdrh2_seq": "IYGGGST", "cdrh3_seq": "ASRLGVRATTGDLDY", "cdrl1_seq": "QSISSW", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYNTYSWWT", "cdrh1_pos": "[21, 28]", "cdrh2_pos": "[46, 52]", "cdrh3_pos": "[91, 105]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "5j3d", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "14N4", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Fusion glycoprotein F0, Human respiratory syncytial virus A", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing mAb 14N4 in complex with F protein"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 2616, 6914, 16, 2607, 15580, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 2753, 9049, 5289, 11424, 17930, 1927, 2616, 5481, 29988, 3413, 43, 18, 1920, 5289, 11424, 17930, 1977, 43, 2921, 51, 4324, 5289, 2213, 1988, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 14606, 3200, 2890, 16, 1956, 2743, 10869, 1988, 24105, 8703, 2037, 2447, 2912, 4092, 12498, 9046, 3200, 2890, 3788, 18, 3], "antigen": ["AIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCCLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLG", "QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQ"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A human Fab, AMG 509 (IGHV1/IGKV3-Kappa), targeting the engineered trimeric Metalloreductase STEAP1 of Homo sapiens. STEAP1 is a tumor-associated antigen expressed in prostate tumors and at elevated levels in metastatic castration-resistant prostate cancer. The antibody is designed as a T-cell engager to redirect T cells toward STEAP1-expressing tumor cells, with avidity-dependent selectivity for high STEAP1 expression on tumor cells relative to normal cells.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASIEWVRQAPGQRLEWMGEDFNEKFQGRVTFTADTSSDTAYMELSSLRSEDTAVYYCWGQGTLVTVSGYTFSTYWILPGSGQTTRWGYYGTRGYFNV", "metadata": {"pdb_id": "8ucd", "light_chain_seq": "EIVLTQSPATLSLSPGERATLSCRASSSVSYMHWFQQKPGQAPRLLIYSTSNLASGIPARFSGSGSGTDYTLTISSLEPEDFAVYYCQQRRSFPYTFGQGTKLEI", "cdrh1_seq": "GYTFSTYW", "cdrh2_seq": "ILPGSGQT", "cdrh3_seq": "TRWGYYGTRGYFNV", "cdrl1_seq": "SSVSY", "cdrl2_seq": "STS", "cdrl3_seq": "QQRRSFPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "8ucd", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "AMG 509", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Metalloreductase STEAP1, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "T-cell engager designed to redirect T cells to kill prostate cancer cells expressing STEAP1"}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 2150, 1029, 30468, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 29177, 8969, 3384, 10410, 4780, 9932, 1927, 16350, 27974, 18, 4780, 9932, 1977, 43, 2798, 17, 2458, 4730, 3198, 1922, 5683, 3861, 1930, 2019, 4664, 2428, 1922, 6476, 24458, 17, 4910, 5683, 2539, 18, 1920, 3533, 1977, 4609, 1966, 43, 62, 17, 2024, 11580, 1005, 1942, 2312, 6264, 62, 2094, 4205, 4780, 9932, 17, 4590, 2798, 2094, 16, 1956, 24673, 17, 3100, 9008, 1958, 2149, 4780, 9932, 2294, 1990, 2798, 2094, 3338, 1942, 2791, 2094, 18, 3], "antigen": ["LFPQWHLPIKIAAIIASLTFLYTLLREVIHPLATSHQQYFYKIPILVINKVLPMVSITLLALVYLPGVIAAIVQLHFPHWLDKWMLTRKQFGLLSFFFAVLHAIYSLSYPMRRSYRYKLLNWAYQQVQQNKEDAWIEHDVWRMEIYVSLGIVGLAILALLAVTSIPSVSDSLTWREFHYIQSKLGIVSLLLGTIHALIFAWNKWIDIKQFVWYTPPTFMIAVFLPIVVLIFKSILFL", "ELFPQWHLPIKIAAIIASLTFLYTLLREVIHPLATSHQQYFYKIPILVINKVLPMVSITLLALVYLPGVIAAIVQLHNKFPHWLDKWMLTRKQFGLLSFFFAVLHAIYSLSYPMRRSYRYKLLNWAYQQVQQNKEDAWIEHDVWRMEIYVSLGIVGLAILALLAVTSIPSVSDSLTWREFHYIQSKLGIVSLLLGTIHALIFAWNKWIDIKQFVWYTPPTFMIAVFLPIVVLIFKSILFL", "LFPQWHLPIKIAAIIASLTFLYTLLREVIHPLATSHQQYFYKIPILVINKVLPMVSITLLALVYLPGVIAAIVQLFPHWLDKWMLTRKQFGLLSFFFAVLHAIYSLSYPMRRSYRYKLLNWAYQQVQQNKEDAWIEHDVWRMEIYVSLGIVGLAILALLAVTSIPSVSDSLTWREFHYIQSKLGIVSLLLGTIHALIFAWNKWIDIKQFVWYTPPTFMIAVFLPIVVLIFKSILFLP"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, 31.a.83 (IGHV3/IGKV3-Kappa), targeting the Hemagglutinin of Influenza A virus. Hemagglutinin is a class I viral fusion protein that binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and mediates fusion of the viral and endosomal membranes during infection. The antibody is designed as a broadly protective neutralizing antibody targeting the conserved HA stem epitope, binding within the HA stem domain.", "target_protein": "EVQLLESGGGLVQPGESLRVSCAASLSWVRQAPGKGLEWVSAYYADTVKGRFTISRDNSQTTLYLQMNSLRADDTATYYCWGKGTTVTVSSSGFTFRDSAISGNGGATAKDESPPIYNLMPGYYSTYYYMDV", "metadata": {"pdb_id": "7u8j", "light_chain_seq": "EIVMTQSPVTLSVSPGETATLSCRASQSVRSNLAWYQQKPGQAPRLLIYGASTRATDIPARFSGSGSGTEFTLSISSLQSDDFAVYYCQQYNHWLRTFGQGTKLEIRTV", "cdrh1_seq": "GFTFRDSA", "cdrh2_seq": "ISGNGGAT", "cdrh3_seq": "AKDESPPIYNLMPGYYSTYYYMDV", "cdrl1_seq": "QSVRSN", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYNHWLRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 119]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5kaq", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "31.a.83", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": "HA stem", "functional_role": "neutralizing", "evidence_quote": "broadly protective antistem antibody"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 3470, 18, 43, 18, 5893, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 18, 26141, 1977, 43, 2921, 51, 4324, 5289, 2213, 1988, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 10412, 5289, 1927, 1920, 4324, 1930, 16514, 5726, 2409, 2909, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 6337, 12130, 3533, 5133, 1920, 5305, 2118, 4402, 10095, 16, 2743, 2651, 1920, 2118, 4402, 3418, 18, 3], "antigen": ["GIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQI", "ATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICRLVDGQTCDIINGALGSPGCDHLNGAEWDVFIERPNAVDTCYPFDVPEYQSLRSILANNGKFEFIAEEFQWNTVKQNGKSGACKRANVDDFFNRLNWLVKSDGNAYPLQNLTKINNGDYARLYIWGVHHPSTSTEQTNLYKNNPGGVTVSTKTSQTSVVPDIGSRPLVREQSGRVSFYWTIVEPGDLIVFNTIGNLIAPRGHYKLNNQKKSTILNTAIPICKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPE"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: An antibody (IGHV1/IGLV1-Lambda) targeting LOX-1, a scavenger receptor implicated in atherosclerosis. This antibody forms a complex with LOX-1.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKVSMHWVRQAPGKGLEWMGGHTHQKFQGRVTMTEDTSTDTAYMELSSLRSEDTAVYYCWGQGTTVTVSSAGYTLTELSFDPEDFKYALVWGTQGKGVRGWDYYYGMDV", "metadata": {"pdb_id": "7r8u", "light_chain_seq": "QSVVTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLIYGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSGWVFGGGTKLTVLGQ", "cdrh1_seq": "GYTLTELS", "cdrh2_seq": "FDPEDFKY", "cdrh3_seq": "ALVWGTQGKGVRGWDYYYGMDV", "cdrl1_seq": "SSNIGAGYD", "cdrl2_seq": "GNS", "cdrl3_seq": "QSYDSSLSGWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 117]", "cdrl1_pos": "[25, 33]", "cdrl2_pos": "[51, 53]", "cdrl3_pos": "[90, 100]", "cdrh3_split": "val", "cdrh3_cluster": "7r8u", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "antibody", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "LOX-1", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 1925, 3533, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 5133, 11846, 17, 21, 16, 43, 21433, 3148, 6835, 1922, 9824, 18, 2052, 3533, 4952, 43, 2796, 1956, 11846, 17, 21, 18, 3], "antigen": ["CSAPCPQDWIWHGENCYLFSSGSFNWEKSQEKCLSLDAKLLKINSTADLDFIQQAISYSSFPFWMGLSRRNPSYPWLWEDGSPLMPHLFRVRGAVSQTYPSGTCAYIQRGAVYAENCILAAFSICQKKANLR", "CSAPCPQDWIWHGENCYLFSSGSFNWEKSQEKCLSLDAKLLKINSTADLDFIQQAISYSSFPFWMGLSRRNPSYPWLWEDGSPLMPHLFRVRGAVSQTYPSGTCAYIQRGAVYAENCILAAFSICQKKANL"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human Fab, A1227 (IGHV3/IGKV1-Kappa), targeting the Major capsid protein P domain of Norovirus Hu/GII.4/Farmington Hills/2004/USA. The Major capsid protein is the structural component of the norovirus capsid. The antibody is designed to achieve broad cross-genogroup binding across GI and GII norovirus strains, recognizing a conserved region at the interface between the P domain and shell domain on the assembled capsid. Please generate the HCDRs for this antibody.", "target_protein": "QVQLVQSGGGMVQPGGSLSLSCAASMTWVRQAPGKGLEWVSSYYADSVKGRFTISRDSSMNTLYLQMSNLRAGDTAVYYCWGQGTTVTVSSAGFTLSNYAIGGSGGTTAKDKTRTLRLGYSGMDV", "metadata": {"pdb_id": "6n81", "light_chain_seq": "DIRLTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPDLLIYGASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFGNYYCQQSFSTPRTFGQGTKVELKRT", "cdrh1_seq": "GFTLSNYA", "cdrh2_seq": "IGGSGGTT", "cdrh3_seq": "AKDKTRTLRLGYSGMDV", "cdrl1_seq": "QSISSY", "cdrl2_seq": "GAS", "cdrl3_seq": "QQSFSTPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6n81", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "A1227", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Major capsid protein, Norovirus Hu/GII.4/Farmington Hills/2004/USA", "target_domain": null, "functional_role": "other", "evidence_quote": "broad cross-reactivity of antibody A1227; broad binding but no blocking activity"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 8080, 4460, 1027, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 3044, 14681, 2213, 58, 3418, 1927, 3990, 7414, 5897, 19, 29262, 18, 24, 19, 22281, 5405, 30115, 19, 4247, 19, 3785, 18, 1920, 3044, 14681, 2213, 1977, 1920, 4346, 4594, 1927, 1920, 3990, 7414, 14681, 18, 1920, 3533, 1977, 4609, 1942, 6230, 4949, 3567, 17, 2065, 16907, 2743, 3436, 7217, 1930, 29262, 3990, 7414, 4046, 16, 15667, 43, 5305, 3031, 2019, 1920, 6854, 2192, 1920, 58, 3418, 1930, 9929, 3418, 1990, 1920, 10151, 14681, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["KPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGTHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIQGMLTQTTRGDGSTRGHKATVSTGDVHFTPKLGSIQFNTDTNNDFETGQNTKFTPVGVVQDGNGAHQNEPQQWVLPSYSGRTGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A synthetic Fab (IGHV3/IGKV1-Kappa) targeting the pH-gated potassium channel KcsA of Streptomyces lividans. The pH-gated potassium channel KcsA acts as a pH-gated potassium ion channel; changing the cytosolic pH from 7 to 4 opens the channel. This antibody is intended as a structural tool to stabilize the channel conformation and facilitate crystallographic studies of the selectivity filter and gating mechanisms.", "target_protein": "VQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWIGENYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGYTFTSDWIIPSYGRAARERGDGYFDY", "metadata": {"pdb_id": "7mjt", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSIGTDIHWYQQKPGKAPKLLIKYASESISGVPSRFSGSRGTDFTLTISLQPEDFATYYCQQSNRWPFTFGQGTKVEIKRT", "cdrh1_seq": "GYTFTSDW", "cdrh2_seq": "IIPSYGRA", "cdrh3_seq": "ARERGDGYFDY", "cdrl1_seq": "QSIGTD", "cdrl2_seq": "YAS", "cdrl3_seq": "QQSNRWPFT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 105]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "7mdj", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "pH-gated potassium channel KcsA, Streptomyces lividans", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "Fab fragments bound in the pore mouth vicinity"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 6830, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 2087, 17, 12336, 9057, 4999, 29971, 1019, 1927, 22874, 15260, 9532, 3355, 18, 1920, 2087, 17, 12336, 9057, 4999, 29971, 1019, 8016, 1966, 43, 2087, 17, 12336, 9057, 4755, 4999, 31, 8546, 1920, 9410, 2087, 2037, 27, 1942, 24, 19851, 1920, 4999, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 1920, 4999, 7748, 1930, 6628, 17832, 2351, 1927, 1920, 9008, 6199, 1930, 12568, 3531, 18, 3], "antigen": ["CAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVVTATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALATWFVGQC"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human Fab, H014 (IGHV1/IGKV6-Kappa), targeting the Spike protein S1 of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors (ACE2, NRP1/NRP2, ASGR1, or integrin) to initiate infection, and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that prevents attachment of SARS-CoV-2 to host cell receptors, binding within the BetaCoV S1-CTD and targeting a conformational epitope accessible when the RBD is in the open conformation. Generate the corresponding HCDRs.", "target_protein": "QLVQSGAEVKKPGATVKISCKVSIHWVKQAPGKSLEWIGYSDNLKFKGAATLTADTSTDTAYMELSSLRSEDTAVYYCWGQGTTVTVSSAGYSFSNYYIDPFNGGTARSEYDPYYVMDY", "metadata": {"pdb_id": "7cah", "light_chain_seq": "IVLTQSPFQSVSPKEKVTITCRASQSISSNLHWYQQKPDQSPKLLIKYASQSISGIPSRFSGSGSGTDFTLTINSLEAEDFGIYFCQQTNFWPYIFGQGTKLEIL", "cdrh1_seq": "GYSFSNYY", "cdrh2_seq": "IDPFNGGT", "cdrh3_seq": "ARSEYDPYYVMDY", "cdrl1_seq": "QSISSN", "cdrl2_seq": "YAS", "cdrl3_seq": "QQTNFWPYI", "cdrh1_pos": "[23, 30]", "cdrh2_pos": "[48, 55]", "cdrh3_pos": "[94, 106]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "7cak", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "H014", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": false, "target_antigen": "Spike protein S1, Severe acute respiratory syndrome coronavirus 2", "target_domain": "BetaCoV S1-CTD", "functional_role": "neutralizing", "evidence_quote": "efficiently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses by engaging the S receptor binding domain"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 6914, 16, 29161, 3745, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 10429, 2213, 4062, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 12, 8298, 1028, 16, 5214, 5113, 19, 5214, 5991, 16, 1966, 2299, 1009, 16, 2014, 8920, 13, 1942, 11051, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 10299, 8576, 1927, 20466, 17, 6083, 17, 22, 1942, 4423, 2024, 4086, 16, 2743, 2651, 1920, 4666, 4879, 1020, 4062, 17, 15898, 1930, 5133, 43, 8523, 10095, 10551, 2469, 1920, 25780, 1977, 1922, 1920, 4437, 7748, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A human Fab, CB017.5 (IGHV3/IGLV3-Lambda), targeting the Major surface glycoprotein G of Human respiratory syncytial virus A. The Major surface glycoprotein G attaches the virion to the host cell membrane by interacting with heparan sulfate and CX3CR1 to initiate infection, and helps the virus escape antibody-dependent restriction by acting as an antigen decoy and modulating leukocyte activity. The antibody is designed as a neutralizing antibody targeting the central conserved region of RSV G to prevent viral attachment and reduce pulmonary inflammation associated with severe RSV disease.", "target_protein": "VQLVESGGGVVQPGRSLRLSCSASMHWVRQAPGQGLEWVAIYYADSVKGRFTISRDNSKETLYLQMNSLRVEDTAVYYCWGQGTTVTVSSAGFTFSVYAIWYDGSNKARDPIVGHTRDGLDV", "metadata": {"pdb_id": "6blh", "light_chain_seq": "SYELTQPPSVSVSPGQTARVTCSGDAMAEQYTYWYQQKPGQAPVLIIFKDTERPSGIPERFSGSSSGTTVTLTISGVQTEDEADYYCQSTDSSGTSWVFGGGTKLTVLGQ", "cdrh1_seq": "GFTFSVYA", "cdrh2_seq": "IWYDGSNK", "cdrh3_seq": "ARDPIVGHTRDGLDV", "cdrl1_seq": "AMAEQY", "cdrl2_seq": "KDT", "cdrl3_seq": "QSTDSSGTSWV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 109]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 97]", "cdrh3_split": "val", "cdrh3_cluster": "6blh", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CB017.5", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "Major surface glycoprotein G, Human respiratory syncytial virus A", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "potently neutralized both subtypes of RSV and protect RSV-challenged animals from severe disease"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 2616, 6914, 16, 5529, 6924, 1027, 18, 25, 12, 20733, 1020, 1010, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 5133, 1920, 3044, 3154, 11424, 49, 1927, 2616, 5481, 29988, 3413, 43, 18, 1920, 3044, 3154, 11424, 49, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 22024, 8767, 1930, 26652, 1942, 11051, 2909, 16, 1930, 12612, 1920, 3413, 11781, 3533, 17, 3100, 7587, 2007, 8290, 1966, 1925, 4730, 25164, 1930, 10871, 11864, 2455, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 4101, 5305, 3031, 1927, 12390, 49, 1942, 4625, 4324, 8576, 1930, 4412, 5352, 4531, 2458, 1956, 4010, 12390, 2573, 18, 3], "antigen": ["DFHFEVFNFVPCSICSNNPTCWAICKRIPNKKPGK"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab, atezolizumab (IGHV3/IGKV1-Kappa), targeting the engineered Ig-like V-type domain of Programmed cell death 1 ligand 1. PD-L1 plays a critical role in induction and maintenance of immune tolerance to self by modulating T-cell activation through interaction with the inhibitory receptor PD-1; blocking this interaction reverses exhausted T-cell phenotype and normalizes anti-tumor response. The antibody is designed to block PD-1/PD-L1 interaction by competing with PD-1 for the same binding surface on PD-L1, binding within the Ig-like V-type domain.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVAWYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSAAGFTFSDSWISPYGGSTARRHWPGGFDY", "metadata": {"pdb_id": "5xxy", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYHPATFGQGTKVEIKRT", "cdrh1_seq": "GFTFSDSW", "cdrh2_seq": "ISPYGGST", "cdrh3_seq": "ARRHWPGGFDY", "cdrl1_seq": "QDVSTA", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYLYHPAT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5xxy", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "atezolizumab", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Programmed cell death 1 ligand 1, Homo sapiens", "target_domain": "Ig-like V-type", "functional_role": "other", "evidence_quote": "blocks PD-1/PD-L1 interaction through competing with PD-1 for the same surface area on PD-L1"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 30280, 13642, 12191, 19240, 3368, 1014, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 7021, 17, 3189, 64, 17, 2601, 3418, 1927, 13839, 2024, 3539, 21, 5207, 21, 18, 3203, 17, 7554, 5705, 43, 4140, 2770, 1922, 4408, 1930, 6291, 1927, 3743, 6555, 1942, 3543, 2007, 10871, 62, 17, 2024, 2936, 2596, 2835, 1956, 1920, 5431, 3148, 3203, 17, 21, 31, 7472, 2052, 2835, 28817, 13246, 2013, 62, 17, 2024, 4629, 1930, 19564, 1036, 2246, 17, 2798, 2644, 18, 1920, 3533, 1977, 4609, 1942, 3367, 3203, 17, 21, 19, 3203, 17, 7554, 2835, 2007, 11743, 1956, 3203, 17, 21, 1958, 1920, 2841, 2743, 3154, 1990, 3203, 17, 7554, 16, 2743, 2651, 1920, 7021, 17, 3189, 64, 17, 2601, 3418, 18, 3], "antigen": ["AFTVTVPKDLYVVEYGSNMTIECKFPVDLAALIVYWEMEDKNIIQFVHGERARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNA"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A human Fab, F005-126 (IGHV1/IGLV1-Lambda), targeting the engineered Hemagglutinin of Influenza A virus (H3N2 strain). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and internalization, and mediates membrane fusion by undergoing a low-pH-induced conformational change in the endosome. The antibody is designed as a broadly neutralizing antibody that recognizes a conserved epitope in the globular head region, including a conserved glycan, and prevents the low-pH-induced conformational change required for membrane fusion. Generate the corresponding HCDRs.", "target_protein": "QVQLVQSGAEVKKPGASVTVSCQVSLSWVRQAPGQGLEWVGWKYVKKFQGRVTMTTHTGTNTAYMEMKSLRSDDTAVYYCWGQGTMVTVSSAGYTLTSYGINTYDGQTARVEGVRGVMGFHYYPMDV", "metadata": {"pdb_id": "3whe", "light_chain_seq": "SVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYAVHWYQQLPGTAPKLLISGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSGSVFGGGTKLTVLGQ", "cdrh1_seq": "GYTLTSYG", "cdrh2_seq": "INTYDGQT", "cdrh3_seq": "ARVEGVRGVMGFHYYPMDV", "cdrl1_seq": "SSNIGAGYA", "cdrl2_seq": "GNS", "cdrl3_seq": "QSYDSSLSGSV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 99]", "cdrh3_split": "val", "cdrh3_cluster": "3whe", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "F005-126", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing human antibody against H3N2 viruses; prevent low-pH-induced conformational changes"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 17930, 15264, 17, 10483, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 11091, 26141, 1927, 7108, 43, 3413, 12, 25234, 3943, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 12071, 16, 1930, 10412, 3260, 5289, 2007, 7258, 43, 2330, 17, 2087, 17, 2719, 8523, 3185, 1922, 1920, 22321, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1988, 16197, 43, 5305, 10095, 1922, 1920, 20975, 4469, 3031, 16, 2710, 43, 5305, 15060, 16, 1930, 10299, 1920, 2330, 17, 2087, 17, 2719, 8523, 3185, 3414, 1958, 3260, 5289, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["STATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWVTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQTRGLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQ"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A murine Fab, 8B2 (IGHV1/IGKV1-Kappa), targeting a non-phosphorylated epitope of Microtubule-associated protein tau from Homo sapiens. Tau promotes microtubule assembly and stability and functions as a linker protein between axonal microtubules and neural plasma membrane components. The antibody is designed to target tau as part of immunotherapeutic approaches in Alzheimer's disease, distinguishing non-phosphorylated tau from phosphorylated pathological forms.", "target_protein": "EVQLQQSGPELVKPGASVKMSCKASIHWVKQKPGQGLEWIGYIYNEKFKGKATLTSDTSSSTVYMELISLTAEDSAVYWCWGQGTTLTVSSAGYTFTSYVIYPYNDGTVRERDNYGVY", "metadata": {"pdb_id": "6dc8", "light_chain_seq": "DVLLTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPELLIYKVSNRFYGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQDSHIPYTFGGGTRLEIKRA", "cdrh1_seq": "GYTFTSYV", "cdrh2_seq": "IYPYNDGT", "cdrh3_seq": "VRERDNYGVY", "cdrl1_seq": "QSIVHSNGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQDSHIPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 105]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "6dc8", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "8B2", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Microtubule-associated protein tau, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "targeting tau with immunotherapies is currently the most common approach taken in clinical trials"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 7135, 6914, 16, 15524, 1028, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 43, 2447, 17, 7199, 10095, 1927, 10544, 17, 2458, 2213, 7462, 2037, 16350, 27974, 18, 7462, 7383, 10544, 5957, 1930, 5057, 1930, 4088, 1966, 43, 11040, 2213, 2192, 10623, 12444, 1930, 5181, 3582, 3260, 4178, 18, 1920, 3533, 1977, 4609, 1942, 2758, 7462, 1966, 3131, 1927, 6595, 2098, 4608, 1984, 1935, 4895, 1922, 9116, 11, 61, 2573, 16, 15589, 2447, 17, 7199, 7462, 2037, 7199, 6598, 4952, 18, 3], "antigen": ["SPRHL"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human IgG (IGHV3/IGKV1-Kappa) targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors, including ACE2, triggering direct fusion at the cell membrane or internalization by endocytosis, and mediates fusion of viral and cellular membranes through conformational changes. The antibody, O5C2, is designed as a broadly neutralizing antibody targeting an unusually large epitope within the receptor-binding domain that overlaps with the ACE2 binding interface. Generate the corresponding HCDRs.", "target_protein": "VQLVESGGGLIQPGGSLRLSCAASMSWVRQAPGKGLEWVSIFYAEPVQGRFTVSRDNSKNTLFLEMNSLRVEDTAVYYCWGQGAMVTVSGIIVSRNYLYAGGSSARDLQWGIDI", "metadata": {"pdb_id": "8xbf", "light_chain_seq": "DIQMTQTPPSLSASVGDRVSISCRASQSTGSWLAWYQQKPGKAPKLLIYKTSSLESGVPSRFSGSGSGTEFTLTISSLQPDDVATYYCQHYDTYSSTFGQGTKVEIKRT", "cdrh1_seq": "GIIVSRNY", "cdrh2_seq": "LYAGGSS", "cdrh3_seq": "ARDLQWGIDI", "cdrl1_seq": "QSTGSW", "cdrl2_seq": "KTS", "cdrl3_seq": "QHYDTYSST", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 55]", "cdrh3_pos": "[94, 103]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8xbf", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "O5C2", "antibody_format": "IgG", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain", "functional_role": "neutralizing", "evidence_quote": "broad-spectrum neutralization against SARS-CoV-2 variants, including EG.5.1"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 5166, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 16, 2710, 8298, 1028, 16, 14074, 3083, 5289, 2019, 1920, 2024, 3260, 2014, 12071, 2007, 11914, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 18, 1920, 3533, 16, 57, 20118, 1028, 16, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1925, 25041, 3103, 10095, 2651, 1920, 3148, 17, 2743, 3418, 1988, 19853, 1956, 1920, 8298, 1028, 2743, 6854, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSTVGGNYNYRYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A murine Fab, ICSM18 (IGHV1/IGKV4-Kappa), targeting the Major prion protein of Homo sapiens. The Major prion protein plays roles in neuronal development, synaptic plasticity, myelin maintenance, and iron homeostasis. This antibody forms a complex with the Major prion protein.", "target_protein": "EVQLQQSGPELVKPGSSVKISCKASLDWVKQSHGKTLEWIGNGYNQKFRGKATLTVDKSSSTAYMELHSLTSEDSAVYYCWGQGTLVTVSSARNTFTDYNVYPNNGVTALYYYDVSY", "metadata": {"pdb_id": "6suz", "light_chain_seq": "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMHWYQQKSGTSPKRWIYDTSKLASGVPARFSGSGSGTSYSLTISSMEAEDAATYFCHQWRSNPYTFGGGTKLEIKRA", "cdrh1_seq": "RNTFTDYN", "cdrh2_seq": "VYPNNGVT", "cdrh3_seq": "ALYYYDVSY", "cdrl1_seq": "SSVSY", "cdrl2_seq": "DTS", "cdrl3_seq": "HQWRSNPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 104]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "2w9e", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ICSM18", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Major prion protein, Homo sapiens", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 7135, 6914, 16, 13772, 8012, 1025, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 16, 5133, 1920, 3044, 16686, 2213, 1927, 16350, 27974, 18, 1920, 3044, 16686, 2213, 5705, 5456, 1922, 5121, 2740, 16, 6251, 8771, 16, 12996, 6291, 16, 1930, 5680, 7622, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 3044, 16686, 2213, 18, 3], "antigen": ["LGVYVLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQ"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A bovine Fab, B77 (IGHV1/IGLV1-Lambda), targeting the VP2 capsid protein of Foot-and-mouth disease virus serotype O/TIBET/99. The antibody is designed as a serotype O-specific neutralizing antibody that blocks virus-receptor interaction via steric hindrance, engaging the VP2 BC-loop and HI-loop near the icosahedral threefold axis of the FMDV capsid. Please provide the HCDR sequences.", "target_protein": "SGPSLVKPSQTLSLTCTISIGWVRQAPGKALEWIGDYYNPALKSRLSITKHNSKSQVRLSVSSVTPEDTATYYCLYGVDAWGGFSLSSYTMSNGGMPAKSRYTGDGSIG", "metadata": {"pdb_id": "7d3k", "light_chain_seq": "ITCSGTYSNVGTGNYVSWFQQIPSAPRTLIYSVTNRASGVPDRFSGSRSGHTATLTISSLQAEDEADYFCLSWQSGNTALFGSGT", "cdrh1_seq": "GFSLSSYT", "cdrh2_seq": "MSNGGMP", "cdrh3_seq": "AKSRYTGDGSIG", "cdrl1_seq": "YSNVGTGNY", "cdrl2_seq": "SVT", "cdrl3_seq": "LSWQSGNTAL", "cdrh1_pos": "[19, 26]", "cdrh2_pos": "[44, 50]", "cdrh3_pos": "[89, 100]", "cdrl1_pos": "[6, 14]", "cdrl2_pos": "[31, 33]", "cdrl3_pos": "[70, 79]", "cdrh3_split": "val", "cdrh3_cluster": "7d3k", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "B77", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "O/TIBET/99 VP2, Foot-and-mouth disease virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "FMDV serotype O-specific neutralizing antibodies (NAbs) (F145 and B77)"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 6970, 6914, 16, 17685, 1027, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 9314, 1028, 14681, 2213, 1927, 8135, 17, 1930, 17, 11701, 2573, 3413, 15306, 57, 19, 8895, 1946, 19, 4922, 18, 1920, 3533, 1977, 4609, 1966, 43, 15306, 57, 17, 2487, 12130, 3533, 1988, 7644, 3413, 17, 3148, 2835, 3454, 17638, 28831, 16, 15888, 1920, 9314, 1028, 6452, 17, 5881, 1930, 10220, 17, 5881, 4931, 1920, 29310, 24704, 23109, 5432, 1927, 1920, 23339, 1020, 14681, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["RILTTRNGHTTSTTQSSVGVTYGYATAEDFVSGPNTSGLETRVVQAERFFKTHLFDWVTSDPFGRCYQLELPTDHKGVYGSLTDSYAYMRNGWDVEVTAVGNQFNGGCLLVAMVPELCSIDKRGLYQLTLFPHQFINPRTNMTAHITVPFVGVNRYDQYKVHKPWTLVVMVVAPLTVNTEGAPQIKVYANIAPTNVHVAGEFPSKE"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, PN-SIA28 (IGHV3/IGKV1-Kappa), targeting the Hemagglutinin of Influenza A virus. Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and internalization, and functions as a class I viral fusion protein responsible for penetration into the cell cytoplasm by mediating membrane fusion. The antibody is designed as a broadly neutralizing antibody targeting a conserved epitope in the fusion domain, capable of inhibiting membrane fusion across diverse influenza A virus subtypes including group 1, group 2, and bat-origin H17 and H18 HAs.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVAGYYADSVKGRFTISRDSSKSTLYLQMNSLRPEDTAVYYCWGQGTTVTVSGFPFSSYGVSYDGSYKARPSAIFGIYIILNGLDV", "metadata": {"pdb_id": "7wvg", "light_chain_seq": "EIVLTQSPSSVSASVGDRVTITCRATQGISSWLAWYQQKPGKPPKLLIFGASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYFCQQAHSFPLTFGGGTKVEIK", "cdrh1_seq": "GFPFSSYG", "cdrh2_seq": "VSYDGSYK", "cdrh3_seq": "ARPSAIFGIYIILNGLDV", "cdrl1_seq": "QGISSW", "cdrl2_seq": "GAS", "cdrl3_seq": "QQAHSFPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7wvd", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "PN-SIA28", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "inhibits membrane fusion mediated by bat-origin H17 and H18 HAs"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 7594, 17, 26352, 4839, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 12071, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 12006, 2460, 1920, 2024, 5239, 2007, 10239, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 43, 5305, 10095, 1922, 1920, 5289, 3418, 16, 7131, 1927, 7918, 3260, 5289, 3436, 6445, 7108, 43, 3413, 8160, 2710, 2210, 21, 16, 2210, 22, 16, 1930, 11579, 17, 4853, 9169, 1027, 1930, 9169, 1025, 2258, 18, 3], "antigen": ["AIAGFIEGGWQGLIDGWYGYHHQNSEGSGYAADKEATQKAVDAITTKVNNIIDKMNTQFESTAKEFNKIEMRIKHLSDRVDDGFLDVWSYNAELLVLLENERTLDFHDANVNNLYQKVKVQLKDNAIDMGNGCFKILHKCNNTCMDDIKNGTYNYYEYRKESHLEKQKID", "DQICIGYHSNNSTQTVNTLLESNVPVTSSHSILEKEHNGLLCKLKGKAPLDLIDCSLPAWLMGNPKCDELLTASEWAYIKEDPEPENGICFPGDFDSLEDLILLVSNTDHFRKEKIIDMTRFSDVTTNNVDSACPYDTNGASFYRNLNWVQQNKGKQLIFHYQNSENNPLLIIWGVHQTSNAAEQNTYYGSQTGSTTITIGEETNTYPLVISESSILNGHSDRINYFWGVVNPNQNFSIVSTGNFIWPEYGYFFQKTTNISGIIKSSEKISDCDTICQTKIGAINSTLPFQNIHQNAIGDCPKYVKAQELVLATGLRNNPIK"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human Fab, CIS42 (IGHV7/IGLV2-Lambda), targeting a peptide epitope from the Circumsporozoite protein of Plasmodium falciparum. The Circumsporozoite protein is essential for sporozoite development, migration through the mosquito vector and host dermis, and infection of host hepatocytes through binding to heparan sulfate proteoglycans. The antibody is designed as a neutralizing antibody to prevent malaria infection by targeting the junctional epitope positioned between the N terminus and central repeat domain of PfCSP.", "target_protein": "VQLVQSGSELKKPGASVKVSCKTSMNWVRQAPGQGLEWMGWTYAPGFTGRFVFSFDTSVSTAYLQISSLKAEDTAVYYCWGQGTLVTVSSAGYTFTTYAINTNTGNPARVYSYGVPFDY", "metadata": {"pdb_id": "6b5t", "light_chain_seq": "SVLTQPASVSGSPGQSITISCTATSSNVGSFNLVSWYQHHPGKAPKLIIHEVSKRPSGASNRFSGSKSGNTASLTISGLQAEDEADYYCCSYVGSDTWVFGGGTKLTVLGQ", "cdrh1_seq": "GYTFTTYA", "cdrh2_seq": "INTNTGNP", "cdrh3_seq": "ARVYSYGVPFDY", "cdrl1_seq": "SSNVGSFNL", "cdrl2_seq": "EVS", "cdrl3_seq": "CSYVGSDTWV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 106]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "6b5r", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CIS42", "antibody_format": "Fab", "heavy_subclass": "IGHV7", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Circumsporozoite protein, Plasmodium falciparum", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "passive transfer conferred high-level, sterile protection against malaria infection"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 6914, 16, 5848, 6852, 12, 20733, 1020, 1027, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 43, 4207, 10095, 2037, 1920, 28868, 2074, 26553, 2213, 1927, 15663, 13098, 18, 1920, 28868, 2074, 26553, 2213, 1977, 4415, 1958, 9130, 26553, 2740, 16, 5049, 2596, 1920, 9719, 4580, 1930, 4423, 20201, 16, 1930, 2909, 1927, 4423, 9919, 2596, 2743, 1942, 22024, 8767, 25185, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1942, 4625, 7505, 2909, 2007, 5133, 1920, 21226, 10095, 11814, 2192, 1920, 56, 7822, 1930, 4101, 6865, 3418, 1927, 14425, 3508, 18, 3], "antigen": ["ANPNANPNANPNA"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A human Fab, CT149 (IGHV1/IGKV3-Kappa), targeting the Hemagglutinin of Influenza A virus (H7N9, A/Anhui/1/2013). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for membrane fusion in the endosome. The antibody is designed as a broadly neutralizing antibody that engages the HA stem region across multiple HA protomers, neutralizing divergent influenza A virus subtypes from both group 1 and group 2 HA lineages. Please generate its HCDRs.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKTSVSWVRQAPGQGPEWVGWDYAQKFQGRVTLTTDATTATAFLDLRSLRPDDTATYFCWGQGTLVIVSSAGYSFSTYGISAYTGITARDKVQGRVEVGSGGRHDY", "metadata": {"pdb_id": "4r8w", "light_chain_seq": "EVVLTQSPGTLALPPGERATLSCRASHRVGSTYIAWYQQKSGQAPRRLIYGASNRATDIPDRFSGSGSGTDFTLTIRRLEPEDSAVYYCQQFSVSPWTFGQGTRVEIKRT", "cdrh1_seq": "GYSFSTYG", "cdrh2_seq": "ISAYTGIT", "cdrh3_seq": "ARDKVQGRVEVGSGGRHDY", "cdrl1_seq": "HRVGSTY", "cdrl2_seq": "GAS", "cdrl3_seq": "QQFSVSPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "4r8w", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CT149", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus (A/Anhui/1/2013, H7N9)", "target_domain": "HA stem region", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibody crosslinking two haemagglutinin monomers"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 3369, 22987, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 12, 16754, 28955, 16, 43, 19, 1925, 24315, 1033, 19, 21, 19, 3871, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 3260, 5289, 1922, 1920, 22321, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1988, 11580, 1036, 1920, 2118, 4402, 3031, 3436, 3137, 2118, 23583, 27306, 16, 12130, 13609, 7108, 43, 3413, 8160, 2037, 2321, 2210, 21, 1930, 2210, 22, 2118, 10439, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["LFGAIAGFIENGWEGLIDGWYGFRHQNAQGEGTAADYKSTQSAIDQITGKLNRLIEKTNQQFELIDNEFNEVEKQIGNVINWTRDSITEVWSYNAELLVAMENQHTIDLADSEMDKLYERVKRQLRENAEEDGTGCFEIFHKCDDDCMASIRNNTYDHSKYREEAMQNR", "DKICLGHHAVSNGTKVNTLTERGVEVVNATETVERTNIPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKEAMGFTYSGIRTNGATSACRRSGSSFYAEMKWLLSNTDNAAFPQMTKSYKNTRKSPALIVWGIHHSVSTAEQTKLYGSGNKLVTVGSSNYQQSFVPSPGARPQVNGLSGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGIQSGVQVDANCEGDCYHSGGTIISNLPFQNIDSRAVGKCPRYVKQRSLLLATGMKNVPE"]} {"modality_type": "antibody", "text": "A rhesus macaque Fab, DH650 (IGHV1/IGKV2-Kappa), targeting the Envelope glycoprotein gp120 of Human immunodeficiency virus 1. The gp120 surface protein attaches the virus to the host lymphoid cell by binding to the primary receptor CD4, inducing structural rearrangement that creates a high-affinity binding site for chemokine coreceptors. The antibody is designed as a neutralizing antibody targeting the CD4 receptor binding site (CD4bs), with recognition mechanisms including HCDR2-mediated CD4 mimicry conserved with human CD4bs broadly neutralizing antibodies. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "QVQLVQSGAEVKKPGASVKLSCKASINWVRQAPGQGLEWMGWGYAQKFQDRVTMTRDTSTSIAYMELGSLRYEDTAVYFCWGQGVPVTVSGAGYGFTIYSINPRNGRITRGQLELTASRFDK", "metadata": {"pdb_id": "6xcj", "light_chain_seq": "DIVMTQSPLSLPVTPGEPAAISCRSSQSLLDRADGNTYLDWYLQKPGQSPQLLIYEVSNRASGVPDRFSGSGSDTDFTLKISRVEAEDVGVYYCMQGLEFPYSFGQGTKVEIKRT", "cdrh1_seq": "GYGFTIYS", "cdrh2_seq": "INPRNGRI", "cdrh3_seq": "TRGQLELTASRFDK", "cdrl1_seq": "QSLLDRADGNTY", "cdrl2_seq": "EVS", "cdrl3_seq": "MQGLEFPYS", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 102]", "cdrh3_split": "val", "cdrh3_cluster": "6xcj", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DH650", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp120, Human immunodeficiency virus 1", "target_domain": "CD4 receptor binding site (CD4bs)", "functional_role": "neutralizing", "evidence_quote": "DH650 lineage mAbs neutralized wildtype CH505 T/F strain"}}}, "tokenized_instruction": [2, 43, 16996, 20533, 6914, 16, 6781, 5964, 1008, 12, 20733, 7390, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 16102, 1927, 2616, 13141, 3413, 21, 18, 1920, 16102, 3154, 2213, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1988, 15628, 43, 2149, 17, 5173, 2743, 3200, 1958, 11673, 30435, 3448, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 4095, 3148, 2743, 3200, 12, 4095, 2083, 13, 16, 1956, 5708, 3531, 2710, 27203, 9746, 17, 3434, 4095, 10223, 6907, 5305, 1956, 2616, 4095, 2083, 11984, 12130, 3788, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["TLFCAPQEMVLKNVTENFNMWKNDMVDQMHEDVISLWDQSLKPCVKLTGGSVIKVSFDPIPIHYCAPAGYAILKCNNKTFTGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEGEIIIRSENITNNVKTIIVHLNESVKIECTRPREAYCNINESKWNETLQRVSKKLKEYFPHKNITFQPSSGGDLEITTHSFNCGGEFFYCNTSSLFNRTYMASTRTITIHCRIKQAGNITCISIITGLLLTRDGGKNNTETFRPGGGNMKDNWRSELYKYKVVEV"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A murine Fab (IGHV5/IGKV3-Kappa) targeting alpha-1-antitrypsin of Homo sapiens. Alpha-1-antitrypsin is a serine protease inhibitor whose major physiological function is protection of the lower respiratory tract against proteolytic destruction by human leukocyte elastase. This antibody forms a complex with the monomeric form of alpha-1-antitrypsin. Please generate its HCDRs.", "target_protein": "DVQLVESGGGLVKPGGSLKLSCAASMSWVRQTPEKRLEWVATYSPDSVKGRFTISRDNAKSTLYLQMSSLKSEDTAMFYCWGQGTSVTVSSAGFTFSSYTISSGGDYTSRAEFITTATWGVYAMDY", "metadata": {"pdb_id": "6hx4", "light_chain_seq": "DIVLTQSPDSLAVSLGQRATISCRASESVDNYGISFMNWFQQKPGQPPKLLIYAASNQGSGVPARFSGSGSGTDFSLNIHPMEEDDTAMYFCQQSKEVPWTFGGGTKLEIKRA", "cdrh1_seq": "GFTFSSYT", "cdrh2_seq": "ISSGGDYT", "cdrh3_seq": "SRAEFITTATWGVYAMDY", "cdrl1_seq": "ESVDNYGISF", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSKEVPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "6hx4", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Alpha-1-antitrypsin, Homo sapiens", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 1020, 1015, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 4595, 17, 21, 17, 10310, 6907, 2523, 1921, 1927, 16350, 27974, 18, 4595, 17, 21, 17, 10310, 6907, 2523, 1921, 1977, 43, 8468, 7154, 4106, 6098, 3044, 5005, 2347, 1977, 6202, 1927, 1920, 2826, 5481, 6482, 3316, 12712, 12102, 2007, 2616, 11864, 23296, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 14457, 2386, 1927, 4595, 17, 21, 17, 10310, 6907, 2523, 1921, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["FNKITPNLAEFAFSLYRQLAHQSNSTNIFFSPVSIATAFAMLSLGTKADTHDEILEGLNFNLTEIPEAQIHEGFQELLRTLSQLQLTTGNGLFLFLEDVKKSEAFTVNFGDKKQINDYVEKGTQGKIVDLVDTVFALVNYIFFKGKWERPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSSWVLLMKYLGNATAIFFLPDEGKLQHLENELTHDIITKFLENEDRRSASLHLPKLSITGTYDLKSVLGQLGITKVFLKLSKAVHKAVLTIDEKGTLEAIPMSIPPEVKFNKPFVFLMIEQNTKSPLFMGKVVNPTQ"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? Human Fabs, ADI-46152 and ADI-58048 (IGHV3/IGKV1-Kappa), targeting GP38 of Crimean-Congo hemorrhagic fever virus strain IbAr10200. GP38 plays a role in virion attachment to host receptor and mediates fusion between viral and cellular membranes after endocytosis. These antibodies are designed to provide cross-clade protective efficacy against multiple CCHFV isolates through Fc-mediated mechanisms, with ADI-46152 targeting the N-terminal three-helix bundle region and ADI-58048 targeting the \u03b2 sandwich region of GP38.", "target_protein": "EVQLVESGGVLVQPGGSLRLSCAASMTWVRQAPGKGLEWVSVYYADSVKGRFAISRDNSKNTVYLQMNSLRVEDTAVYYCWGQGTLVTVSSGFTVNSNYIYSGGYTARLRLSSSWYPEAFDY", "metadata": {"pdb_id": "8vww", "light_chain_seq": "AILLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGRAPKVLIYDASSLANGVPSRFSGSGSGTDFTLTINSLQPEDFATYYCQQFNYYPLTFGGGTKVEIK", "cdrh1_seq": "GFTVNSNY", "cdrh2_seq": "IYSGGYT", "cdrh3_seq": "ARLRLSSSWYPEAFDY", "cdrl1_seq": "QGISSA", "cdrl2_seq": "DAS", "cdrl3_seq": "QQFNYYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8vww", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "GP38, Crimean-Congo hemorrhagic fever virus strain IbAr10200", "target_domain": null, "functional_role": "other", "evidence_quote": "non-neutralizing protective antibodies often function through Fc-mediated mechanisms"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 2616, 6914, 1036, 16, 2041, 1033, 17, 4182, 22249, 1930, 2041, 1033, 17, 25195, 6301, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 4882, 4745, 1927, 20598, 1928, 17, 27450, 16052, 9087, 3413, 3943, 27931, 7011, 11636, 2283, 18, 4882, 4745, 5705, 43, 2770, 1922, 19230, 8576, 1942, 4423, 3148, 1930, 10412, 5289, 2192, 4324, 1930, 3689, 5726, 2256, 11914, 18, 2144, 3788, 2032, 4609, 1942, 3394, 3567, 17, 11315, 6337, 4348, 3316, 3137, 21846, 19414, 5645, 2596, 6437, 17, 3434, 3531, 16, 1956, 2041, 1033, 17, 4182, 22249, 5133, 1920, 56, 17, 4262, 2559, 17, 7864, 14142, 3031, 1930, 2041, 1033, 17, 25195, 6301, 5133, 1920, 161, 18038, 3031, 1927, 4882, 4745, 18, 3], "antigen": ["NLKMEIILTLSQGLKKYYGKILRLLQLTLEEDTEGLLEWCKRNLGLDCDDTFFQKRIEEFFITGEGHFNEVLQFRTPAEPFKSYFAKGFLSIDSGYYSAKCYSGTSNSGLQLINITRHSTRIVDTPGPKITNLKTINCINLKASIFKEHREVEINVLLPQVAVNLSNCHVVIKSHVCDYSLDIDGAVRLPHIYHEGVFIPGTYKIVIDKKNKLNDRCTLFTDCVIKGREVRKGQSVLRQYKTEIRIG"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A rat Fab, 9D7 (IGHV1/IGKV3-Kappa), targeting an engineered human Interleukin-10 monomer. Interleukin-10 is a major immune regulatory cytokine that acts on many cells of the immune system with profound anti-inflammatory functions, binding to its heterotetrameric receptor (IL-10RA and IL-10RB) to drive STAT3-mediated phosphorylation and expression of anti-inflammatory mediators. The antibody is designed as a neutralizing antibody that blocks IL-10 receptor engagement through an allosteric mechanism.", "target_protein": "QVNLLQSGAALVKPGASVKLSCKASIHWVKQSHGKSLEWIGYNYNEKFKNKATLTVDKSTSTGYMELSRLTSEDSANYSCWGQGTLVTVSSAGYTFTDFYINPNSGYTTRGVPGNNWFPY", "metadata": {"pdb_id": "1lk3", "light_chain_seq": "DTVLTQPPALTVSPGEKLTISCKASESVTSRMHWYQQKPGQQPKLLIYKASNLASGVPARFSGSGSGTDFTLTIDPVEADDTAIYFCQQSWNGPLTFGAGTKLELKRA", "cdrh1_seq": "GYTFTDFY", "cdrh2_seq": "INPNSGYT", "cdrh3_seq": "TRGVPGNNWFPY", "cdrl1_seq": "ESVTSR", "cdrl2_seq": "KAS", "cdrl3_seq": "QQSWNGPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "1lk3", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "9D7", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Interleukin-10, Homo sapiens", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing Fab fragment; antagonism of the IL-10M1/IL-10R1 interaction"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 3067, 6914, 16, 29, 29678, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1925, 11091, 2616, 9198, 17, 2119, 11287, 18, 9198, 17, 2119, 1977, 43, 3044, 3743, 4948, 6137, 1988, 8016, 1990, 3086, 2094, 1927, 1920, 3743, 2433, 1956, 11098, 2246, 17, 3769, 4088, 16, 2743, 1942, 2496, 19732, 28959, 17118, 3148, 12, 2614, 17, 2119, 5524, 1930, 2614, 17, 2119, 16007, 13, 1942, 9265, 8919, 17, 3434, 4050, 1930, 2294, 1927, 2246, 17, 3769, 9744, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 2614, 17, 2119, 3148, 9577, 2596, 1925, 14772, 2856, 18, 3], "antigen": ["NMLRDLRDAFSRVKTFFQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCEKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMK"]} {"modality_type": "antibody", "text": "What would be the HCDR sequences of an antibody with the following function: A human Fab (IGHV1/IGLV3-Lambda) targeting the Transmembrane glycoprotein (gp41) of Human immunodeficiency virus 1. The gp41 transmembrane glycoprotein mediates fusion of viral and host cell membranes during HIV-1 entry. The antibody is designed as a neutralizing antibody targeting the conserved N-heptad repeat (N-HR) epitope, which is exposed during the conformational changes preceding membrane fusion and represents an attractive target for broadly neutralizing antibodies across diverse HIV-1 strains.", "target_protein": "QLVQSGAEVKKPGSSVKVSCKASFSWVRQAPGQGLEWMGSVYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCWGQGTLVTVSSAGGTFNSYAIIPLFGFVARYFDTYNNYGFAN", "metadata": {"pdb_id": "3mac", "light_chain_seq": "IELTQPPSVSVVPGQTARISCSGDNIPYEYASWYQQKPGQAPVLVIYGDNNRPSGIPERFSGSNSGNTATLTISGTQAEDEADYYCASWDSMTVDGVFGGGTKLTVLGQ", "cdrh1_seq": "GGTFNSYA", "cdrh2_seq": "IIPLFGFV", "cdrh3_seq": "ARYFDTYNNYGFAN", "cdrl1_seq": "NIPYEY", "cdrl2_seq": "GDN", "cdrl3_seq": "ASWDSMTVDGV", "cdrh1_pos": "[23, 30]", "cdrh2_pos": "[48, 55]", "cdrh3_pos": "[94, 107]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 96]", "cdrh3_split": "val", "cdrh3_cluster": "4khx", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "Transmembrane glycoprotein (gp41), Human immunodeficiency virus 1", "target_domain": "N-heptad repeat (N-HR)", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibodies...broadly neutralizing across a wide range of primary isolates from subtype B and C HIV-1"}}}, "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 28961, 1020, 1010, 17, 18279, 13, 5133, 1920, 9117, 11424, 12, 25618, 13, 1927, 2616, 13141, 3413, 21, 18, 1920, 25618, 9117, 11424, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 3525, 17, 21, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 5305, 56, 17, 20662, 2015, 6865, 12, 56, 17, 3668, 13, 10095, 16, 2154, 1977, 4616, 2409, 1920, 8523, 2840, 12141, 3260, 5289, 1930, 4972, 1925, 10974, 2758, 1958, 11984, 12130, 3788, 3436, 6445, 3525, 17, 21, 4046, 18, 3], "antigen": ["MQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILATTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLEGGQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARITWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLEGQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARIL"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human Fab, CAP228-16H (IGHV5/IGLV3-Lambda), targeting the V1V2 domain of HIV-1 Envelope. The V1V2 region is a target of vaccine-elicited and infection-induced antibodies that can block viral interactions with the \u03b14\u03b27 integrin, a non-essential but pathogenesis-relevant adhesion receptor. The antibody is designed to recognize the \u03b1-helical helix-coil conformation of V1V2 that presents both the primary and secondary \u03b14\u03b27 binding determinants, thereby blocking integrin engagement and mediating antiviral protection.", "target_protein": "EVQLVQSGAEVKKPGESLKISCKGSIGWVRQVPGKGLEWMGIRYRASFQGQVTISADQSSNTAYLQWSSLKASDTAMYYCWGQGTMVTVSSAGYRFPSSWIYPGDGETARHGRGVREVINAFDI", "metadata": {"pdb_id": "6fy2", "light_chain_seq": "YELTQPPSVSVAPGTTATITCGGVDIGSTLVHWYQQRPGQAPLLVIYDDSDRPSGIPERFSGSNSGNMATLTISRVEAGDEADYYCQVWHSTSAVIFGGGTKLTVLSQ", "cdrh1_seq": "GYRFPSSW", "cdrh2_seq": "IYPGDGET", "cdrh3_seq": "ARHGRGVREVINAFDI", "cdrl1_seq": "DIGSTL", "cdrl2_seq": "DDS", "cdrl3_seq": "QVWHSTSAVI", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6fy1", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CAP228-16H", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "CAP225 Scaffolded V1V2, Human immunodeficiency virus 1", "target_domain": null, "functional_role": "other", "evidence_quote": "block the binding of HIV-1 to \u03b14\u03b27 integrin by recognising a common helix-coil epitope"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 6914, 16, 2853, 24894, 17, 2641, 1023, 12, 20733, 1020, 1015, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 5133, 1920, 11217, 15755, 3418, 1927, 3525, 17, 21, 11262, 18, 1920, 11217, 15755, 3031, 1977, 43, 2758, 1927, 5955, 17, 9856, 1930, 2909, 17, 2719, 3788, 1988, 2112, 3367, 4324, 3719, 1956, 1920, 17623, 1110, 1027, 8920, 16, 43, 2447, 17, 4415, 2308, 6559, 17, 4494, 6141, 3148, 18, 1920, 3533, 1977, 4609, 1942, 9967, 1920, 160, 17, 11514, 7864, 17, 9121, 7748, 1927, 11217, 15755, 1988, 8178, 2321, 1920, 3065, 1930, 4067, 17623, 1110, 1027, 2743, 9873, 16, 6113, 7472, 8920, 9577, 1930, 10239, 10129, 6202, 18, 3], "antigen": ["EIRDKKQEVRALFYRSDIVPLK"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (Omicron variant, S-6P-RRAR). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors such as ACE2, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. This antibody forms a complex with the Spike glycoprotein.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7xco", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 7254, 1935, 2830, 6031, 16, 61, 17, 26, 1034, 17, 5162, 1933, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 2427, 1966, 8298, 1028, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 11424, 18, 3], "antigen": ["QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVIKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDMESEFRVYSSANNCTFEYVSQPFLNFKNLREFVFKNIDGYFKIYSKHTPIDLPQGFSALEPLVDLPIGINITRFQTLLALHRSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A rhesus macaque Fab, DH1338 (IGHV4/IGKV3-Kappa), targeting the Spike protein S1 of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors such as ACE2, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. This antibody forms a complex with the Spike protein S1, binding within the Receptor-binding domain (RBD). Please generate the HCDRs for this antibody.", "target_protein": "QLQLQESGPGLVKPSETLSLTCAVSWSWIRQPPGKGLGWIGRDYNPSLKSRVTISTDTSKNQFSLKLSSVTAADTAVYYCWGQGLRVTVSSGGSISRKNISGSGGSTARVAYYEDDYGYYYTEGAFDF", "metadata": {"pdb_id": "8dpz", "light_chain_seq": "EIVMTQSPATLSLSPGERATLSCRTSQSVSSYVAWYQQKPEQTPRLLIYDASSRATGIPDRFSGGGSGTDFTLTISSLEPEDFAVYYCQQYSNWPWTFGQGTKVEIK", "cdrh1_seq": "GGSISRKN", "cdrh2_seq": "ISGSGGST", "cdrh3_seq": "ARVAYYEDDYGYYYTEGAFDF", "cdrl1_seq": "QSVSSY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYSNWPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 116]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8dpz", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DH1338", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike protein S1, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 16996, 20533, 6914, 16, 6781, 13041, 1025, 12, 20733, 1020, 1006, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 10429, 2213, 4062, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 2427, 1966, 8298, 1028, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 2213, 4062, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKS"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A rat Fab (IGHV2/IGLV3-Lambda) targeting the engineered T-cell surface protein tactile (CD96) of Mus musculus. T-cell surface protein tactile promotes NK cell-target adhesion by interacting with PVR present on target cells and may function during the late phase of the immune response. This antibody is designed as a surrogate research tool to block CD155 ligand engagement with CD96, binding within the Ig-like V-type 1 domain.", "target_protein": "VQLKESGPGLVQPSQTLSLTCTVSVSWIRQPPGKGLEWMGVDYNSAIKSRLSITRDTSKSQVFLKMNSLQTEDTAMYFCWGQGTLVTVSSAGLSLTNNIIWSNGGTASRDYPGFAY", "metadata": {"pdb_id": "7s13", "light_chain_seq": "ELIQPPSSSVTLGSTVSLTCVGDELPKRYAYWYQQKPDQSIVRVIYEDSKRPSGISDRFSGSSSGTTATLTIRDAQAEDEADYYCLSTYSDDKLPIFGGGTKLTVLGQ", "cdrh1_seq": "GLSLTNNI", "cdrh2_seq": "IWSNGGT", "cdrh3_seq": "ASRDYPGFAY", "cdrl1_seq": "ELPKRY", "cdrl2_seq": "EDS", "cdrl3_seq": "LSTYSDDKLPI", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 55]", "cdrh3_pos": "[94, 103]", "cdrl1_pos": "[23, 28]", "cdrl2_pos": "[46, 48]", "cdrl3_pos": "[85, 95]", "cdrh3_split": "val", "cdrh3_cluster": "7s13", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "T-cell surface protein tactile, Mus musculus", "target_domain": "Ig-like V-type 1", "functional_role": "other", "evidence_quote": "surrogate antibody blocking CD155 ligand engagement to mouse CD96"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 3067, 6914, 12, 20733, 15755, 19, 28961, 1020, 1010, 17, 18279, 13, 5133, 1920, 11091, 62, 17, 2024, 3154, 2213, 18607, 12, 2464, 10352, 13, 1927, 3177, 25795, 1957, 18, 62, 17, 2024, 3154, 2213, 18607, 7383, 5916, 2024, 17, 2758, 6141, 2007, 8615, 1956, 24783, 2481, 1990, 2758, 2094, 1930, 2278, 2347, 2409, 1920, 5058, 3193, 1927, 1920, 3743, 2644, 18, 2052, 3533, 1977, 4609, 1966, 43, 13475, 2659, 5229, 1942, 3367, 29218, 7054, 5207, 9577, 1956, 2464, 10352, 16, 2743, 2651, 1920, 7021, 17, 3189, 64, 17, 2601, 21, 3418, 18, 3], "antigen": ["GVWEELFNVGDDVYALPGSDINLTCQTKEKNFLVQMQWSKVTDKNDMIALYHPQYGLYCGQEHACESQVAATETEKGVTNWTLYLRNISSALGGKYECIFTLYPEGIKTTVYNLIVE"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A murine Fab (IGHV1/IGKV4-Kappa) targeting Sulfhydryl oxidase 1 of Mus musculus. Sulfhydryl oxidase 1 catalyzes the oxidation of sulfhydryl groups in peptide and protein thiols to disulfides and plays a role in disulfide bond formation in extracellular proteins and extracellular matrix assembly. This antibody is intended as a structural tool to enable crystallization of a QSOX1 cis-proline mutant variant. Please generate its HCDRs.", "target_protein": "QVQLQQSGPELVKPGASVKISCKASIHWVKQRPGQGLEWIGWEYSEKFKGKATLTADTSSSTAYMQLSSLTSEDSAVYYCWGQGTLVTVSASGYSFTSYYIYPGSYNTARSEDWFAY", "metadata": {"pdb_id": "6hf1", "light_chain_seq": "QIVLTQSPAIMSASPGEKVTISCSASSSVSYMYWYHQKPGSSPKPWIYRTSNLASGVPARFSGSGSGTSYSLTISSMEAEDAATYYCQQYHSYPLTFGAGTKLELKRT", "cdrh1_seq": "GYSFTSYY", "cdrh2_seq": "IYPGSYNT", "cdrh3_seq": "ARSEDWFAY", "cdrl1_seq": "SSVSY", "cdrl2_seq": "RTS", "cdrl3_seq": "QQYHSYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 104]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "5d93", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Sulfhydryl oxidase 1, Mus musculus", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "crystallized in complex with an antibody Fab fragment after other approaches did not yield crystals"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 30011, 2199, 10488, 21, 1927, 3177, 25795, 1957, 18, 30011, 2199, 10488, 21, 17097, 1920, 6638, 1927, 30011, 2199, 2671, 1922, 4207, 1930, 2213, 27383, 1942, 11830, 1036, 1930, 5705, 43, 2770, 1922, 11830, 5403, 3337, 1922, 5329, 2697, 1930, 5329, 4526, 5957, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 8675, 15416, 1927, 43, 15178, 23599, 5848, 17, 12958, 3606, 6031, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["VLYSSSDPLTLLDADSVRPTVLGSSSAWAVEFFASWCGACIAFAPTWKELANDVKDWRPALNLAVLDCAEETNSAVCREFNIAGFTTVRFFQAFTKNGSGATLPGAGANVQTLRMRLIDALESHRDTWPPACPPLEPAKLNDIDGFFTRNKADYLALVFEREDSYLGREVTLDLSQYHAVAVRRVLNTESDLVNKFGVTDFPSCYLLLRNGSVSRVPVLVESRSFYTSYLRGLPGLTR"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2, specifically the Receptor-binding domain (RBD). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. This antibody forms a complex with the Spike glycoprotein RBD of the Omicron BA.2.86 variant.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "8y6a", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 16, 4475, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 11424, 25780, 1927, 1920, 7254, 1935, 2830, 6813, 18, 22, 18, 5713, 6031, 18, 3], "antigen": ["NLCPFHEVFNATRFASVYAWNRTRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIKGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKHSGNYDYWYRLFRKSKLKPFERDISTEIYQAGNKPCKGKGPNCYFPLQSYGFRPTYGVGHQPYRVVVLSFE"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A human Fab, PN-SIA28 (IGHV3/IGKV1-Kappa), targeting the Hemagglutinin of Influenza A virus H18 from bat (A/flat-faced bat/Peru/033/2010). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for membrane fusion by mediating conformational changes in HA2 upon low pH exposure in endosomes. The antibody is designed as a broadly neutralizing antibody targeting the conserved stem region of HA, capable of neutralizing divergent group 1 and group 2 influenza A virus subtypes including bat H17 and H18 viruses by inhibiting HA-mediated membrane fusion and blocking HA0 maturation. Please generate its HCDRs.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVAGYYADSVKGRFTISRDSSKSTLYLQMNSLRPEDTAVYYCWGQGTTVTVSGFPFSSYGVSYDGSYKARPSAIFGIYIILNGLDV", "metadata": {"pdb_id": "8gv7", "light_chain_seq": "EIVLTQSPSSVSASVGDRVTITCRATQGISSWLAWYQQKPGKPPKLLIFGASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYFCQQAHSFPLTFGGGTKVEIK", "cdrh1_seq": "GFPFSSYG", "cdrh2_seq": "VSYDGSYK", "cdrh3_seq": "ARPSAIFGIYIILNGLDV", "cdrl1_seq": "QGISSW", "cdrl2_seq": "GAS", "cdrl3_seq": "QQAHSFPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7wvd", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "PN-SIA28", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Hemagglutinin H18, Influenza A virus (A/flat-faced bat/Peru/033/2010(H18N11))", "target_domain": "stem region", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibody against both endemic influenza A and emerging pathogens such as bat H17 and H18 viruses"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 7594, 17, 26352, 4839, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 9169, 1025, 2037, 11579, 12, 43, 19, 9778, 17, 17293, 11579, 19, 23189, 19, 23343, 19, 3657, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 3260, 5289, 2007, 10239, 8523, 2840, 1922, 2118, 1028, 4073, 2330, 2087, 3395, 1922, 14978, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 5305, 4402, 3031, 1927, 2118, 16, 7131, 1927, 12130, 13609, 2210, 21, 1930, 2210, 22, 7108, 43, 3413, 8160, 2710, 11579, 9169, 1027, 1930, 9169, 1025, 6241, 2007, 7918, 2118, 17, 3434, 3260, 5289, 1930, 7472, 2118, 1008, 7655, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["AIAGFIEGGWQGLIDGWYGYHHQNSEGSGYAADKEATQKAVDAITTKVNNIIDKMNTQFESTAKEFNKIEMRIKHLSDRVDDGFLDVWSYNAELLVLLENERTLDFHDANVNNLYQKVKVQLKDNAIDMGNGCFKILHKCNNTCMDDIKNGTYNYYEYRKESHLEKQKID", "DQICIGYHSNNSTQTVNTLLESNVPVTSSHSILEKEHNGLLCKLKGKAPLDLIDCSLPAWLMGNPKCDELLTASEWAYIKEDPEPENGICFPGDFDSLEDLILLVSNTDHFRKEKIIDMTRFSDVTTNNVDSACPYDTNGASFYRNLNWVQQNKGKQLIFHYQNSENNPLLIIWGVHQTSNAAEQNTYYGSQTGSTTITIGEETNTYPLVISESSILNGHSDRINYFWGVVNPNQNFSIVSTGNFIWPEYGYFFQKTTNISGIIKSSEKISDCDTICQTKIGAINSTLPFQNIHQNAIGDCPKYVKAQELVLATGLRNNPIK"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A murine Fab, vFP16.02 (IGHV1/IGKV1-Kappa), targeting the Fusion peptide of Human immunodeficiency virus 1. The Fusion peptide is part of the Envelope glycoprotein gp160, which attaches the virus to the host lymphoid cell and mediates fusion of viral and host cell membranes during entry. The antibody is designed as a vaccine-elicited broadly neutralizing antibody targeting the Fusion peptide, binding within the Fusion peptide domain. What would the HCDRs be?", "target_protein": "QVQLLQSGAELVRPGASVTLSCKASIHWVKQTPVRGLDWIGAASNQKVKGRAILTADKSSSTAYMELRSLTSEDSAVYYCWGTGTTVTVSSAGYAFSDYEFDPKSGASTRLRYFGYFDV", "metadata": {"pdb_id": "6wwc", "light_chain_seq": "DVLMTQTPLSLPVSLGGQASISCRSSQSVVYSDGDTYLEWYLQKPGQKPKLLIYKVSRRFSGVPDRFSGSGSGTDFTLKISRVETEDLGVYYCFQGSHVPYTFGGGTKLEIKRT", "cdrh1_seq": "GYAFSDYE", "cdrh2_seq": "FDPKSGAS", "cdrh3_seq": "TRLRYFGYFDV", "cdrl1_seq": "QSVVYSDGDTY", "cdrl2_seq": "KVS", "cdrl3_seq": "FQGSHVPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "6wx2", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "vFP16.02", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Fusion peptide, Human immunodeficiency virus 1", "target_domain": "Fusion peptide", "functional_role": "neutralizing", "evidence_quote": "vaccine-elicited anti-FP antibody...broadly neutralizing antibody"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 7135, 6914, 16, 15691, 5113, 1016, 18, 5725, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 5289, 4207, 1927, 2616, 13141, 3413, 21, 18, 1920, 5289, 4207, 1977, 3131, 1927, 1920, 11262, 11424, 4882, 16954, 16, 2154, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 1930, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 5955, 17, 9856, 11984, 12130, 3533, 5133, 1920, 5289, 4207, 16, 2743, 2651, 1920, 5289, 4207, 3418, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["AVGIGAVF"]} {"modality_type": "antibody", "text": "I want an antibody that has the function: A human Fab, AB-3467 (IGHV4/IGKV1-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor, initiating infection and mediating fusion of viral and cellular membranes. The antibody is designed as a neutralizing antibody targeting the conserved class 4 epitope within the Receptor-binding domain (RBD), with the objective of blocking ACE2 binding and maintaining neutralization breadth across diverse sarbecovirus RBDs and SARS-CoV-2 variants of concern. Output the HCDRs.", "target_protein": "QVQLQESGPGLVKPSETLSLTCTVSWNWIRQPPGKGLEWIGYNYNPSLKSRVSISTDTSKNQFSLKLSSVTAADTAVYYCWGQGTMVTVSSAGGSISSYHIYYSGNTVREMRRGYSGYDYWDLYAFDI", "metadata": {"pdb_id": "7msq", "light_chain_seq": "DIQLTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPNLLIYAASTLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQQLNSYPHTFGQGTKLEIKRT", "cdrh1_seq": "GGSISSYH", "cdrh2_seq": "IYYSGNT", "cdrh3_seq": "VREMRRGYSGYDYWDLYAFDI", "cdrl1_seq": "QGISSY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQLNSYPHT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 115]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7msq", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "AB-3467", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "AB-3467 potently neutralized lentiviral particles bearing SARS CoV1 or CoV2 spike proteins and retained live CoV2 virus neutralization potency against each of the current CoV2 variants of concern"}}}, "tokenized_instruction": [2, 51, 12914, 1925, 3533, 1988, 2258, 1920, 2347, 30, 43, 2616, 6914, 16, 2186, 17, 26955, 1027, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 16, 12410, 2909, 1930, 10239, 5289, 1927, 4324, 1930, 3689, 5726, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 5305, 2921, 24, 10095, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 1956, 1920, 4470, 1927, 7472, 8298, 1028, 2743, 1930, 8231, 14377, 22532, 3436, 6445, 9851, 12409, 7414, 25780, 1036, 1930, 20466, 17, 6083, 17, 22, 4936, 1927, 8353, 18, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFETVCGPK"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A human Fab, chAb-45 (IGHV1/IGKV6-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting the receptor-binding domain (RBD), with potential for combination in a therapeutic antibody cocktail to prevent and treat SARS-CoV-2 infection.", "target_protein": "EVQLQQSGPELVKPGASVKISCKTSIYWVKQSLGKSLEWIGGTYKQFFKGKATLTVDKSSSTAYMELRSLTSEDSAVYYCWGQGTSVTVSSGYTFTEYTNNPNNDDTARDGYPYYYALDF", "metadata": {"pdb_id": "7f63", "light_chain_seq": "DIVMTQSQKFMSTSVGDRVSVTCKSSQNVGTNVAWYQQKPGQSPKALIYSASYRYSGVPDHFTGSGSGTDFTLTISNVQSADLAEYFCQQYNNYPWTFGGGTKLEIKRT", "cdrh1_seq": "GYTFTEYT", "cdrh2_seq": "NNPNNDDT", "cdrh3_seq": "ARDGYPYYYALDF", "cdrl1_seq": "QNVGTN", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYNNYPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7w9e", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "chAb-45", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "potently neutralize authentic SARS-CoV-2 infection according to the plaque reduction neutralization test"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 2616, 6914, 16, 13297, 1014, 17, 3607, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 1956, 2889, 1958, 3921, 1922, 43, 4272, 3533, 12719, 1942, 4625, 1930, 2297, 20466, 17, 6083, 17, 22, 2909, 18, 3], "antigen": ["PNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKS"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human Fab, panitumumab (IGHV4/IGKV1-Kappa), targeting the engineered Epidermal growth factor receptor of Homo sapiens. The Epidermal growth factor receptor is a receptor tyrosine kinase that binds ligands of the EGF family and activates multiple downstream signaling cascades including RAS-RAF-MEK-ERK, PI3 kinase-AKT, PLCgamma-PKC, and STATs pathways. The antibody is designed to block EGFR signaling for treatment of metastatic colorectal cancer, with particular attention to maintaining binding affinity against the S468R resistance mutation that confers acquired resistance in other anti-EGFR therapies.", "target_protein": "QVQLQESGPGLVKPSETLSLTCTVSWTWIRQSPGKGLEWIGHNYNPSLKSRLTISIDTSKTQFSLKLSSVTAADTAIYYCWGQGTMVTVSSAGGSVSSGDYYIYYSGNTVRDRVTGAFDI", "metadata": {"pdb_id": "5sx5", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQHFDHLPLAFGGGTKVEIKRT", "cdrh1_seq": "GGSVSSGDYY", "cdrh2_seq": "IYYSGNT", "cdrh3_seq": "VRDRVTGAFDI", "cdrl1_seq": "QDISNY", "cdrl2_seq": "DAS", "cdrl3_seq": "QHFDHLPLA", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5sx5", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "panitumumab", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Epidermal growth factor receptor, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "panitumumab target the epidermal growth factor receptor for the treatment of metastatic colorectal cancer"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 6914, 16, 3797, 13378, 6683, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 9844, 2905, 2991, 3148, 1927, 16350, 27974, 18, 1920, 9844, 2905, 2991, 3148, 1977, 43, 3148, 6941, 4016, 1988, 6876, 6908, 1927, 1920, 4451, 3416, 1930, 9094, 3137, 5863, 3197, 15967, 2710, 6520, 17, 12783, 17, 12551, 17, 7770, 16, 21197, 4016, 17, 5496, 16, 12897, 4223, 28262, 17, 8425, 16, 1930, 3156, 1036, 3873, 18, 1920, 3533, 1977, 4609, 1942, 3367, 5775, 3197, 1958, 2311, 1927, 6476, 7820, 2539, 16, 1956, 3278, 4976, 1942, 8231, 2743, 5173, 3316, 1920, 6934, 6735, 1005, 3554, 3979, 1988, 16556, 5815, 3554, 1922, 2303, 2246, 17, 5775, 6565, 18, 3], "antigen": ["KKVCNGIGIGEFKDSLSIDATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLDITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIIRNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSHH"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human Fab, 1F04 (IGHV3/IGKV3-Kappa), targeting the Neuraminidase of Influenza A virus (A/Moscow/10/1999 H3N2). Neuraminidase catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates, facilitating virus release and spread through the circulation. The antibody is designed to confer protection against influenza infection through dual mechanisms: viral growth inhibition via steric hindrance of substrate binding and ADCC-mediated cellular cytotoxicity, binding within the Head of neuraminidase on the underside of the head domain. The antibody targets a conserved epitope across multiple H3N2 strains spanning decades. Please generate the HCDRs for this antibody.", "target_protein": "EVQLVESGGGLVLPGRSLRLSCVASMNWVRQAPGTGLEWLSYYYAESVKGRFTISRDNAKNSLYLQMNGLRAEDTATYYCWGQGTLVTVSGFDFSSFEISGNGDTIARQRSVYSTSRSNWSVFLDD", "metadata": {"pdb_id": "8ez7", "light_chain_seq": "EIVLTQSPGTLSLSPGESATLSCRASQSLAPNYLAWFQQQPGQAPRLLIYGASSRAAGIPDRFSGSGSGTDFTLTITRLEPEDFAVYYCQQYGGSPPYTFGQGTKVEIKR", "cdrh1_seq": "GFDFSSFE", "cdrh2_seq": "ISGNGDTI", "cdrh3_seq": "ARQRSVYSTSRSNWSVFLDD", "cdrl1_seq": "QSLAPNY", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYGGSPPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "8ez7", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "1F04", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Neuraminidase, Influenza A virus (A/Moscow/10/1999 H3N2)", "target_domain": "Head of neuraminidase", "functional_role": "other", "evidence_quote": "confer prophylactic and therapeutic protection in vivo via viral growth inhibition and ADCC"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 14078, 14743, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 29831, 1927, 7108, 43, 3413, 12, 43, 19, 7500, 4879, 1018, 19, 2119, 19, 5372, 25234, 13, 18, 29831, 17097, 1920, 6025, 1927, 4262, 20436, 2687, 4248, 2037, 4324, 1930, 3689, 4235, 30378, 2209, 16, 12440, 3413, 4012, 1930, 6441, 2596, 1920, 9255, 18, 1920, 3533, 1977, 4609, 1942, 7909, 6202, 3316, 7108, 2909, 2596, 7064, 3531, 30, 4324, 2905, 3523, 3454, 17638, 28831, 1927, 4510, 2743, 1930, 25899, 17, 3434, 3689, 8470, 16, 2743, 2651, 1920, 4469, 1927, 29831, 1990, 1920, 3302, 2261, 1927, 1920, 4469, 3418, 18, 1920, 3533, 4845, 43, 5305, 10095, 3436, 3137, 25234, 4046, 13346, 8995, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["AEYRNWSKPQCNITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNGHSNDTVHDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCVTGDDENATASFIYNGRLVDSIGSWSKKILRTQESECVCINGTCTVVMTDGSASGKADTKILFIEEGKIVHTSPLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNRPIVDINVKDYSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDVWMGRTISEKLRSGYETFKVIEGWSKPNSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETEVLWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab (IGHV1/IGLV2-Lambda) targeting the Envelope glycoprotein gp120 of Human immunodeficiency virus 1, specifically the CD4 receptor binding site (CD4bs). The gp120 surface protein attaches the virus to the host lymphoid cell by binding to the primary receptor CD4, inducing structural rearrangement that creates a high-affinity binding site for chemokine coreceptors. This antibody is designed as a broadly neutralizing antibody targeting the CD4bs, a conserved epitope class, with particular attention to accommodating N-linked glycans at positions N197 and N276 that frame the recessed CD4bs pocket.", "target_protein": "VQLVQSGAQVKKPGASVTVSCTASMHWVRQAPGQGLEWMGWKYAQKFRGRVSMTRDTSIEIFYMELSRLRSDDTAVYYCWGQGTLVTVSSAGYTFTGYHINPFRGAVAREMFDSSADWSPWRGMVA", "metadata": {"pdb_id": "9ehm", "light_chain_seq": "SALTQPASVSGSPGQSITISCTGSSRDVGGFDLVSWYQQHPGKAPKLMIYEVSKRPSGVSNRFSASKSGNTASLTISGLQAEDEADYYCYSYADGVAFGGGTKLTVLGQ", "cdrh1_seq": "GYTFTGYH", "cdrh2_seq": "INPFRGAV", "cdrh3_seq": "AREMFDSSADWSPWRGMVA", "cdrl1_seq": "SRDVGGFDL", "cdrl2_seq": "EVS", "cdrl3_seq": "YSYADGVA", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 113]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9ehm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp120, Human immunodeficiency virus 1", "target_domain": "CD4 receptor binding site (CD4bs)", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibodies against conserved HIV-1 Env epitopes"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 28961, 15755, 17, 18279, 13, 5133, 1920, 11262, 11424, 16102, 1927, 2616, 13141, 3413, 21, 16, 4475, 1920, 4095, 3148, 2743, 3200, 12, 4095, 2083, 13, 18, 1920, 16102, 3154, 2213, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1988, 15628, 43, 2149, 17, 5173, 2743, 3200, 1958, 11673, 30435, 3448, 18, 2052, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 4095, 2083, 16, 43, 5305, 10095, 2921, 16, 1956, 3278, 4976, 1942, 11852, 2287, 56, 17, 4624, 15509, 2019, 6490, 13007, 8528, 1930, 9585, 10308, 1988, 7673, 1920, 3169, 5590, 1919, 4095, 2083, 10154, 18, 3], "antigen": ["NLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNIGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV"]} {"modality_type": "antibody", "text": "Output the HCDRs for an antibody that performs this function: A human Fab, p60.12 (IGHV1/IGLV2-Lambda), targeting the Pro-secreted protein ORF2 of Hepatitis E virus rat/R63/DEU/2009. The Pro-secreted protein ORF2 forms an icosahedral capsid with T=1 symmetry and 34 nm diameter composed of 60 copies, and plays a role in inhibition of host antibody-mediated neutralization. The antibody is designed as a glycan-sensitive broadly neutralizing antibody that recognizes the non-glycosylated form of pORF2 present in infectious particles.", "target_protein": "VQLVQSGAEVKKPGSSVKVSCKASISWVRQAPGQGLEWMGGNYAPKFQDTVTITADKSTNTVYMEMRSLRSEDTAVYYCWGQGTLVTVSSASSYVIIPIIGTAASNVQLQRRGNWFDP", "metadata": {"pdb_id": "8pmx", "light_chain_seq": "ALTQPASVSGSPGQSITISCTGTSSDIGDYNFVSWYQQHPGKAPKLMIFDVTNRPSGVSNRFSGSKSGNTASLTISGLQVEDEADYYCSSYTSTNTPVVFGGGTKLTVLGQ", "cdrh1_seq": "SSYV", "cdrh2_seq": "IIPIIGTA", "cdrh3_seq": "ASNVQLQRRGNWFDP", "cdrl1_seq": "SSDIGDYNF", "cdrl2_seq": "DVT", "cdrl3_seq": "SSYTSTNTPVV", "cdrh1_pos": "[24, 27]", "cdrh2_pos": "[45, 52]", "cdrh3_pos": "[91, 105]", "cdrl1_pos": "[23, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "8pmx", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "p60.12", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Pro-secreted protein ORF2, Hepatitis E virus rat/R63/DEU/2009", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "potent and broadly neutralizing human antibodies targeting a quaternary epitope"}}}, "tokenized_instruction": [2, 6647, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 17436, 2052, 2347, 30, 43, 2616, 6914, 16, 21139, 1008, 18, 2369, 12, 20733, 7390, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 1965, 17, 8366, 2213, 11234, 1028, 1927, 7977, 47, 3413, 3067, 19, 22098, 1010, 19, 2028, 1032, 19, 3712, 18, 1920, 1965, 17, 8366, 2213, 11234, 1028, 4952, 1925, 29310, 24704, 14681, 1956, 62, 33, 21, 12572, 1930, 3540, 2943, 5483, 7179, 1927, 3276, 9425, 16, 1930, 5705, 43, 2770, 1922, 3523, 1927, 4423, 3533, 17, 3434, 14377, 18, 1920, 3533, 1977, 4609, 1966, 43, 15060, 17, 4532, 11984, 12130, 3533, 1988, 16197, 1920, 2447, 17, 17514, 2386, 1927, 4572, 6680, 2481, 1922, 7465, 5569, 18, 3], "antigen": ["DKPAPARPITNWRSGDVVWVTLPSAEYAQSQSAMGSHPAYWSEEATIINVATGQRALVSSIKWDQVTLNGKVLHKETHSGLVYYQLPLMGKISFWQQGTTKAGYTYNYNTTDSDSLWVWWDGTSKGYLYVSTYTTMLGAGPVNITGLGAIGPSP"]} {"modality_type": "antibody", "text": "A human Fab, C158 (IGHV1/IGLV1-Lambda), targeting the Secreted protein ORF2 of Hepatitis E virus genotype 1. The Secreted protein ORF2 forms an icosahedral capsid and mediates viral entry through interactions with host cell surface proteoglycans and receptors. The antibody is designed as a neutralizing antibody targeting antigenic site 1 of the E2s domain to confer cross-protective immunity against diverse hepatitis E virus genotypes. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "QVQIVQSGAEVKKPGASVKVSCTASLVWVRQAPGQGLEWMGSIYSEKFQGRVSITRDTSASTTYMELRSLRYEDTAVYFCWGNGTTVSVTSGYTFTRYGINTGNANTARERGGSVVEPAAHYMDV", "metadata": {"pdb_id": "9jij", "light_chain_seq": "QSVLTQPPSVSAAPGQKVTISCSGHSSNIANNYVAWYQQLPGTAPKLLIYDNDKRPSGIPDRFSASKSGTSATLGITGLQTGDEAHYYCETWDSSLSLWVFGGGTMVTVL", "cdrh1_seq": "GYTFTRYG", "cdrh2_seq": "INTGNANT", "cdrh3_seq": "ARERGGSVVEPAAHYMDV", "cdrl1_seq": "SSNIANNY", "cdrl2_seq": "DND", "cdrl3_seq": "ETWDSSLSLWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 99]", "cdrh3_split": "val", "cdrh3_cluster": "9jij", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "C158", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": false, "target_antigen": "Secreted protein ORF2, Hepatitis E virus genotype 1", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "cross-reactive antibodies targeting antigenic site 1 can offer protection against rHEV infection"}}}, "tokenized_instruction": [2, 43, 2616, 6914, 16, 29832, 1025, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 8366, 2213, 11234, 1028, 1927, 7977, 47, 3413, 5619, 21, 18, 1920, 8366, 2213, 11234, 1028, 4952, 1925, 29310, 24704, 14681, 1930, 10412, 4324, 6904, 2596, 3719, 1956, 4423, 2024, 3154, 25185, 1930, 4086, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 14606, 3200, 21, 1927, 1920, 6602, 1036, 3418, 1942, 7909, 3567, 17, 6337, 7611, 3316, 6445, 7977, 47, 3413, 7059, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["RPFSVLRANDVLWLSLTAAEYDQSTYGSSTGPVYVSDSVTLVNVATGAQAVARSLDWTKVTLDGRPLSTIQQYSKTFFVLPLRGKLSFWEAGTTKAGYPYNYNTTASDQLLVENAAGHRVAISTYTTSLGAGPVSISAVAVLAPHSA"]} {"modality_type": "antibody", "text": "A human Fab, M15 (IGHV4/IGKV3-Kappa), targeting the engineered stabilized S2 subunit of the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The S2 subunit mediates fusion of the virion and cellular membranes by functioning as a class I viral fusion protein, containing two viral fusion peptides unmasked after cleavage. The antibody is designed to bind broadly across sarbecoviruses to the conserved S2 domain, targeting a central interface epitope at inter-protomer contacts in the prefusion spike trimer. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "QVQLRESGPGLVKPSETLSLTCTVSWSWIRQPPGKGLEWIGYNYNPSLKSRVTISVSTSKNQFSLNLTSVTAADTAVYYCWGQGTLVTVSSAGGSTSGYYIYDIGSTARGFDS", "metadata": {"pdb_id": "9mpw", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQSVSSIYLAWYQQKPGQAPRLLIFAASSRAIGIPDRFSGSGSGTDFTLTISRLEAEDFAVYYCHQYGSSPWTFGQGTKVEIKRT", "cdrh1_seq": "GGSTSGYY", "cdrh2_seq": "IYDIGST", "cdrh3_seq": "ARGFDS", "cdrl1_seq": "QSVSSIY", "cdrl2_seq": "AAS", "cdrl3_seq": "HQYGSSPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 100]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "9mpw", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "M15", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein S2 subunit, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "other", "evidence_quote": "M15 bound broadly to sarbecoviruses but did not neutralize SARS-CoV-2 variants in vitro"}}}, "tokenized_instruction": [2, 43, 2616, 6914, 16, 8510, 1015, 12, 20733, 1020, 1006, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 12017, 5159, 5903, 1927, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 5159, 5903, 10412, 5289, 1927, 1920, 19230, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 16, 3165, 2288, 4324, 5289, 5320, 30370, 1919, 2256, 6404, 18, 1920, 3533, 1977, 4609, 1942, 4566, 11984, 3436, 9851, 12409, 18368, 1942, 1920, 5305, 5159, 3418, 16, 5133, 43, 4101, 6854, 10095, 2019, 2107, 17, 23583, 9213, 9070, 1922, 1920, 9328, 2670, 10429, 20085, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["SNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQFGGFNFSQILPDPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTIQIPFPMQMAYRFEGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNFLVKQLSSNCGAISSVEAEVQIQRLITCRLQSLQTYVTQMLIRAAEYRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPE"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with the host ACE2 receptor and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding. This antibody forms a complex with the Spike protein S1, binding within the Receptor-binding domain (RBD).", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "8df5", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 1920, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 2213, 4062, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 3], "antigen": ["PNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKK"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human Fab (IGHV4/IGKV1-Kappa) targeting the Receptor tyrosine-protein kinase erbB-3 (HER3). HER3 is a cell surface receptor for neuregulins that plays an essential role in myeloid cell differentiation and is involved in heterodimerization with HER2 in breast cancer tumorigenesis. The antibody is designed to bind a unique epitope on HER3 domain I, partially blocking neuregulin-1 ligand binding and disrupting HER2/HER3 heterodimerization to suppress tumor growth in combination with HER2-targeted therapy. What would the HCDRs be?", "target_protein": "QVQLQESGPGLVKPSETLSLTCTVSWNWIRQPFGKGLEWMGYNFNPSLKNRVTISRDTSKNQFSLKLSSVTAADTAVYYCWGQGTTVTVSSAGYSITSAYYISYDGRNARDGDYDAFDY", "metadata": {"pdb_id": "8yry", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQDISNYLNWYQQKPGKAPKLLIYYTSILHSGVPSRFSGSGSGTDYTFTISSLQPEDIATYFCQQGDTLPPTFGGGTKLEIKRT", "cdrh1_seq": "GYSITSAYY", "cdrh2_seq": "ISYDGRN", "cdrh3_seq": "ARDGDYDAFDY", "cdrl1_seq": "QDISNY", "cdrl2_seq": "YTS", "cdrl3_seq": "QQGDTLPPT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8yry", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Receptor tyrosine-protein kinase erbB-3, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "DB-1310 combined with trastuzumab synergistically inhibit breast cancer cell proliferation and tumor growth"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 6914, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 3148, 6941, 17, 2213, 4016, 11954, 17, 23, 12, 3656, 1010, 13, 18, 3656, 1010, 1977, 43, 2024, 3154, 3148, 1958, 2974, 6541, 19962, 1988, 5705, 1925, 4415, 2770, 1922, 9677, 2024, 4155, 1930, 1977, 3286, 1922, 15672, 2466, 1956, 9162, 1922, 3739, 2539, 11472, 18, 1920, 3533, 1977, 4609, 1942, 4566, 43, 5008, 10095, 1990, 3656, 1010, 3418, 51, 16, 6426, 7472, 2974, 6541, 3392, 17, 21, 5207, 2743, 1930, 17214, 9162, 19, 3656, 1010, 15672, 2466, 1942, 4400, 2798, 2905, 1922, 3921, 1956, 9162, 17, 5154, 3181, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["NADLSFLQWIREVNEFSTLPLPNLRVVRGTNSSHALRQLRLTQLTEILSGGVYIEKNDKLCHMDTIDWDNGRSCPPCHEVCKGRCWGPGSEDCQTL"]} {"modality_type": "antibody", "text": "What would be the HCDR sequences of an antibody with the following function: A human Fab (IGHV4/IGKV4-Kappa) targeting human Activin receptor type-2B. Activin receptor type-2B is a transmembrane serine/threonine kinase that forms an activin receptor complex with type-1 receptors to transduce activin signals regulating neuronal differentiation, hair follicle development, FSH production, wound healing, and extracellular matrix production. This antibody is intended as a structural tool to stabilize and facilitate crystallization of activin ligand-receptor complexes, binding to ActRIIB without interfering with ligand binding.", "target_protein": "QLQLQESGPGLVKPSETLSLTCTVSWGWIRQPPGKGLEWIGSYYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCWGQGTTVTVSSAGGSISSSSYYISYSGSTARDSLRYGMDV", "metadata": {"pdb_id": "7oly", "light_chain_seq": "DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYALAPPRTFGGGTKVEIKRT", "cdrh1_seq": "GGSISSSSYY", "cdrh2_seq": "ISYSGST", "cdrh3_seq": "ARDSLRYGMDV", "cdrl1_seq": "QSVLYSSNNKNY", "cdrl2_seq": "WAS", "cdrl3_seq": "QQYALAPPRT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 107]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 103]", "cdrh3_split": "val", "cdrh3_cluster": "7mrz", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Activin receptor type-2B, Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "non-neutralizing Fab fragment that binds to ActRIIB...yielded several crystallographic hits"}}}, "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1006, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 2616, 21797, 3148, 2601, 17, 5751, 18, 21797, 3148, 2601, 17, 5751, 1977, 43, 9117, 8468, 19, 13143, 4016, 1988, 4952, 1925, 21797, 3148, 2796, 1956, 2601, 17, 21, 4086, 1942, 30334, 21797, 4771, 6773, 5121, 4155, 16, 7018, 14792, 2740, 16, 13540, 3372, 16, 6376, 7872, 16, 1930, 5329, 4526, 3372, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 1930, 6628, 15416, 1927, 21797, 5207, 17, 3148, 5048, 16, 2743, 1942, 4033, 21094, 1014, 2979, 13369, 1956, 5207, 2743, 18, 3], "antigen": ["TRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPEAG"]} {"modality_type": "antibody", "text": "A human Fab (IGHV3/IGKV1-Kappa) targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (B.1.427/epsilon variant). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. This antibody, S2L20, is intended as a structural tool to stabilize the N-terminal domain (NTD) in cryo-EM studies of the trimeric spike. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "EVQLVESGGGVVQPGGSLRLSCAASMHWVRQAPGKGLEWVAFYYADSVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCWGQGTLVTVSGFTFNSYGIRYDGGNKANLKDSRYSGSYYDY", "metadata": {"pdb_id": "7n8i", "light_chain_seq": "VIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKVDF", "cdrh1_seq": "GFTFNSYG", "cdrh2_seq": "IRYDGGNK", "cdrh3_seq": "ANLKDSRYSGSYYDY", "cdrl1_seq": "QDIRFY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYDNLPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9c44", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "N-terminal domain (NTD)", "functional_role": "structural_tool", "evidence_quote": "S2L20 was used to stabilize the NTDs"}}}, "tokenized_instruction": [2, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 44, 18, 21, 18, 28133, 19, 22206, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 2052, 3533, 16, 5159, 11232, 1008, 16, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 1920, 56, 17, 4262, 3418, 12, 22078, 13, 1922, 15822, 17, 2391, 2351, 1927, 1920, 29177, 10429, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNRVYSSANNCTFEYVSQPFLFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSF"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A human Fab, N60-I3 (IGHV4/IGLV2-Lambda), targeting the Envelope glycoprotein gp120 of Human immunodeficiency virus 1 (clade A/E). The gp120 surface protein attaches the virus to the host lymphoid cell by binding to the primary receptor CD4, inducing structural rearrangement that creates a high-affinity binding site for chemokine coreceptors. The antibody is designed to mediate ADCC-dependent protection against HIV-1 infection by targeting the cluster A epitope region within the gp41-reactive inner domain of gp120, binding within the Human immunodeficiency virus 1 envelope glycoprotein Gp120.", "target_protein": "EVQLVESGPGLVKPSQTLSLTCTVSWSWIRQHPGKGLEWIGNYYNPSLKSRLTISVDTTQNQFSLKLTSVTAADTAVYYCWGQGTLVTVSSAGASISSGGYFIYYIGNTARVPRLRGGNYFDS", "metadata": {"pdb_id": "4rfo", "light_chain_seq": "QSVLTQPASVSGSPGQSITISCTGTSSDVGGYKYVSWYQQHPDKAPKLMIYEVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTWVFGGGTKLTVLGQ", "cdrh1_seq": "GASISSGGYF", "cdrh2_seq": "IYYIGNT", "cdrh3_seq": "ARVPRLRGGNYFDS", "cdrl1_seq": "SSDVGGYKY", "cdrl2_seq": "EVS", "cdrl3_seq": "SSYTSSSTWV", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 110]", "cdrl1_pos": "[25, 33]", "cdrl2_pos": "[51, 53]", "cdrl3_pos": "[90, 99]", "cdrh3_split": "val", "cdrh3_cluster": "5kjr", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "N60-I3", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp120, Human immunodeficiency virus 1", "target_domain": "Human immunodeficiency virus 1 envelope glycoprotein Gp120", "functional_role": "other", "evidence_quote": "FcR-mediated effector functions of antibodies, including antibody-dependent cell-mediated cytotoxicity (ADCC)"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 2616, 6914, 16, 29077, 1008, 17, 51, 1010, 12, 20733, 1020, 1006, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 11262, 11424, 16102, 1927, 2616, 13141, 3413, 21, 12, 11315, 43, 19, 47, 13, 18, 1920, 16102, 3154, 2213, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1988, 15628, 43, 2149, 17, 5173, 2743, 3200, 1958, 11673, 30435, 3448, 18, 1920, 3533, 1977, 4609, 1942, 8265, 25899, 17, 3100, 6202, 3316, 3525, 17, 21, 2909, 2007, 5133, 1920, 4377, 43, 10095, 3031, 2651, 1920, 25618, 17, 6079, 6671, 3418, 1927, 16102, 16, 2743, 2651, 1920, 2616, 13141, 3413, 21, 11262, 11424, 16102, 18, 3], "antigen": ["VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCIKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes during entry. The antibody is designed as a neutralizing antibody that maintains binding and protective activity across diverse SARS-CoV-2 Omicron variants, binding within the Receptor-binding domain (RBD). Please output the HCDRs.", "target_protein": "VQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "8fxb", "light_chain_seq": "IVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKV", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 114]", "cdrl1_pos": "[25, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "S309 neutralizing antibody; sotrovimab protects against BQ.1.1 and XBB.1.5"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 16566, 2743, 1930, 6337, 2455, 3436, 6445, 20466, 17, 6083, 17, 22, 7254, 1935, 2830, 4936, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["LCPFHEVFNATTFASVYAWNRKRISNCVADYSVFFAFKCTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGSNCYSPLQSYGFRPTYGVGHQPYRVVVLSF"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A murine Fab, Ky15.10 (IGHV3/IGKV1-Kappa), targeting the Circumsporozoite protein of Plasmodium falciparum (isolate NF54). The Circumsporozoite protein is essential for sporozoite development, migration through the vector and host, and infection of host hepatocytes through binding to heparan sulfate proteoglycans on hepatocyte surfaces. The antibody is designed as a neutralizing antibody that inhibits sporozoite traversal and parasite liver invasion, adopting the 1210-like binding mode that confers cross-reactivity to junctional PfCSP repeat motifs.", "target_protein": "QVQLVESGGGVVQPGRSLRLSCAASMHWVRQVPGKGLEWVAIYYADSVKGRFSVSRDNSENTLYLQMSNLRAEDTAVYYCWGQGTTVTVSSAGFTFSNSGIWYDGSNKVRAYFDSENLYDYYGMDV", "metadata": {"pdb_id": "8fb7", "light_chain_seq": "DIQMTQSPSTLSASVGDRVTITCRASQSISRWLAWFQKKPGKAPKLLIYTASNLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYYNYWTFGQGTKVEVKRT", "cdrh1_seq": "GFTFSNSG", "cdrh2_seq": "IWYDGSNK", "cdrh3_seq": "VRAYFDSENLYDYYGMDV", "cdrl1_seq": "QSISRW", "cdrl2_seq": "TAS", "cdrl3_seq": "QQYYNYWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "8fa6", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Ky15.10", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Circumsporozoite protein, Plasmodium falciparum (isolate NF54)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "effectively inhibited Pf sporozoite traversal in vitro and reduced parasite liver load in vivo"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 7135, 6914, 16, 13995, 3962, 18, 2119, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 28868, 2074, 26553, 2213, 1927, 15663, 13098, 12, 9158, 4651, 5651, 13, 18, 1920, 28868, 2074, 26553, 2213, 1977, 4415, 1958, 9130, 26553, 2740, 16, 5049, 2596, 1920, 4580, 1930, 4423, 16, 1930, 2909, 1927, 4423, 9919, 2596, 2743, 1942, 22024, 8767, 25185, 1990, 14675, 7553, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7042, 9130, 26553, 27480, 1923, 1930, 8652, 3568, 6254, 16, 20478, 1920, 11844, 1008, 17, 3189, 2743, 5754, 1988, 16556, 3567, 17, 8229, 1942, 21226, 14425, 3508, 6865, 8277, 18, 3], "antigen": ["DPNANPNVDPNAN"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human Fab (IGHV3/IGKV1-Kappa) targeting GP38, the envelopment polyprotein of Crimean-Congo hemorrhagic fever virus strain IbAr10200. GP38 plays a role in virion attachment to the host receptor and mediates fusion between viral and cellular membranes following endocytosis. This antibody forms a complex with GP38 within the context of the engineered GP38-Gn-Gc heterotrimeric glycoprotein complex in its prefusion conformation. Can you generate its HCDRs?", "target_protein": "EVQLVESGGVLVQPGGSLRLSCAASMTWVRQAPGKGLEWVSVYYADSVKGRFAISRDNSKNTVYLQMNSLRVEDTAVYYCWGQGTLVTVSSGFTVNSNYIYSGGYTARLRLSSSWYPEAFDY", "metadata": {"pdb_id": "9b8j", "light_chain_seq": "AILLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGRAPKVLIYDASSLANGVPSRFSGSGSGTDFTLTINSLQPEDFATYYCQQFNYYPLTFGGGTKVEIK", "cdrh1_seq": "GFTVNSNY", "cdrh2_seq": "IYSGGYT", "cdrh3_seq": "ARLRLSSSWYPEAFDY", "cdrl1_seq": "QGISSA", "cdrl2_seq": "DAS", "cdrl3_seq": "QQFNYYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8vww", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "GP38 (Envelopment polyprotein), Crimean-Congo hemorrhagic fever virus strain IbAr10200", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 4882, 4745, 16, 1920, 9840, 2017, 6240, 5684, 1927, 20598, 1928, 17, 27450, 16052, 9087, 3413, 3943, 27931, 7011, 11636, 2283, 18, 4882, 4745, 5705, 43, 2770, 1922, 19230, 8576, 1942, 1920, 4423, 3148, 1930, 10412, 5289, 2192, 4324, 1930, 3689, 5726, 2894, 11914, 18, 2052, 3533, 4952, 43, 2796, 1956, 4882, 4745, 2651, 1920, 4491, 1927, 1920, 11091, 4882, 4745, 17, 9005, 17, 5469, 27042, 19103, 11424, 2796, 1922, 2496, 9328, 2670, 7748, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["KMEIILTLSQGLKKYYGKILRLLQLTLEEDTEGLLEWCKRNLGLDCDDTFFQKRIEEFFITGEGHFNEVLQFRAEPFKSYFAKGFLSIDSGYYSAKCYSGTSNSGLQLINITRHSTRIVDTPGPKITNLKTINCINLKASIFKEHREVEINVLLPQVAVNLSNCHVVIKSHVCDYSLDIDGAVRLPHIYHEGVFIPGTYKIVIDKKNKLNDRCTLFTDCVIKGREVRKGCSVLRQYKTEIRIG"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A human Fab, CT149 (IGHV1/IGKV3-Kappa), targeting the Hemagglutinin of Influenza A virus. Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for penetration into the cell cytoplasm by mediating membrane fusion. The antibody is designed as a broadly neutralizing antibody against divergent influenza A virus subtypes from both group 1 and group 2 HA lineages, binding within the HA stem region and engaging multiple protomers of the trimeric hemagglutinin.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKTSVSWVRQAPGQGPEWVGWDYAQKFQGRVTLTTDATTATAFLDLRSLRPDDTATYFCWGQGTLVIVSSAGYSFSTYGISAYTGITARDKVQGRVEVGSGGRHDY", "metadata": {"pdb_id": "4ubd", "light_chain_seq": "VVLTQSPGTLALPPGERATLSCRASHRVGSTYIAWYQQKSGQAPRRLIYGASNRATDIPDRFSGSGSGTDFTLTIRRLEPEDSAVYYCQQFSVSPWTFGQGTRVEIKRT", "cdrh1_seq": "GYSFSTYG", "cdrh2_seq": "ISAYTGIT", "cdrh3_seq": "ARDKVQGRVEVGSGGRHDY", "cdrl1_seq": "HRVGSTY", "cdrl2_seq": "GAS", "cdrl3_seq": "QQFSVSPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[25, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "4r8w", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "CT149", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": "HA stem region", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibody with potent efficacy against H3N2 and H7N9 viruses"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 3369, 22987, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 26141, 1927, 7108, 43, 3413, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 12006, 2460, 1920, 2024, 5239, 2007, 10239, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 3316, 13609, 7108, 43, 3413, 8160, 2037, 2321, 2210, 21, 1930, 2210, 22, 2118, 10439, 16, 2743, 2651, 1920, 2118, 4402, 3031, 1930, 15888, 3137, 23583, 27306, 1927, 1920, 29177, 26141, 18, 3], "antigen": ["IENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKG", "STATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQT"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A human Fab, RUPA-55 (IGHV3/IGKV3-Kappa), targeting the engineered Gametocyte surface protein P230 domain 1 of Plasmodium falciparum. The Gametocyte surface protein P230 is required for male and female gamete fusion, male gamete exflagellation, and interaction with host erythrocytes. The antibody is designed to block parasite transmission to mosquitoes through complement-dependent mechanisms, targeting a highly conserved epitope on Pfs230 D1 that is genetically preserved across diverse P. falciparum field isolates.", "target_protein": "DVQLVESGGGLVKPGGSLRLSCAASMNWVRQAPGKGLEWVSSYYADSVKGRFTISRDNAKNSLFLQMDSLRAEDTAVYYCWGQGTLVTVSPAGFTFNSYTISTNIRYIATIAGPLSLKGDFFFDS", "metadata": {"pdb_id": "7uvi", "light_chain_seq": "EIVMTQSPATLSVSPGERATLSCRASQSVSSSLAWYQQKPGQAPRLLIHGASTRATGIPTRFSGSGSGTEFTLTISSLQSEDFAVYYCQQYANWPPWTFGQGTKVESKRT", "cdrh1_seq": "GFTFNSYT", "cdrh2_seq": "ISTNIRYI", "cdrh3_seq": "ATIAGPLSLKGDFFFDS", "cdrl1_seq": "QSVSSS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYANWPPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "7uvi", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "RUPA-55", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Gametocyte surface protein P230, Plasmodium falciparum", "target_domain": null, "functional_role": "other", "evidence_quote": "potent transmission-reducing activity; complement-dependent TRA"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 2616, 6914, 16, 7212, 4302, 17, 4288, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 21009, 4463, 3154, 2213, 7535, 4294, 3418, 21, 1927, 15663, 13098, 18, 1920, 21009, 4463, 3154, 2213, 7535, 4294, 1977, 3414, 1958, 4005, 1930, 4232, 21009, 1021, 5289, 16, 4005, 21009, 1021, 1975, 20631, 30439, 16, 1930, 2835, 1956, 4423, 14161, 18, 1920, 3533, 1977, 4609, 1942, 3367, 8652, 5303, 1942, 13667, 2596, 5508, 17, 3100, 3531, 16, 5133, 43, 3626, 5305, 10095, 1990, 11133, 4553, 1008, 8524, 1988, 1977, 9517, 10502, 3436, 6445, 58, 18, 13098, 3559, 5645, 18, 3], "antigen": ["LSYETTESGDTAVSEDSYDKYASQNTNKEYVCDFTDQLKPTESGPKVKKCEVKVNEPLIKVKIICPLKGSVEKLYDNIEYVPKKSPYVVLTKEETKLKEKLLSKLIYGLLISPTVNEKENNFKEGVIEFTLPPVVHKATVFYFICDNSKTEDDNKKGNRGIVEVYVEPYGGSLKENLYFQGWSHP"]} {"modality_type": "antibody", "text": "What would be the HCDR sequences of an antibody with the following function: A human Fab (IGHV3/IGKV3-Kappa), one of two antibodies in a complex (17C7 and 1112-1), targeting the Glycoprotein of Rabies virus strain Pasteur vaccin. The Glycoprotein attaches the virus to host cellular receptors and induces endocytosis; in the endosome, acidic pH triggers conformational changes that promote fusion between virus and cell membrane. The antibody is designed as a neutralizing antibody that stabilizes the prefusion conformation to prevent the pH-triggered conformational transition required for membrane fusion.", "target_protein": "EVQLVESGGGVVQPGRSLRLSCAASMHWVRQAPGKGLEWVAVDYADSVKGRFTISRDNSKNTLYLQMNSLRTEDTAVYFCWGQGTLVTVSSGFTFSTYAVSYDGRTKARERFSGAYFDY", "metadata": {"pdb_id": "8a1e", "light_chain_seq": "EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYSCQQRNNWPPTFGGGTKVEIKRA", "cdrh1_seq": "GFTFSTYA", "cdrh2_seq": "VSYDGRTK", "cdrh3_seq": "ARERFSGAYFDY", "cdrl1_seq": "QSVSSY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQRNNWPPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8a1e", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Glycoprotein, Rabies virus strain Pasteur vaccin", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "17C7 inhibits pre- to post-fusion conformational transition"}}}, "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 2340, 1927, 2288, 3788, 1922, 43, 2796, 12, 2752, 1030, 1027, 1930, 10118, 1028, 17, 21, 13, 16, 5133, 1920, 11424, 1927, 21508, 3413, 3943, 24868, 4117, 1921, 18, 1920, 11424, 5823, 1918, 1920, 3413, 1942, 4423, 3689, 4086, 1930, 6387, 11914, 31, 1922, 1920, 22321, 16, 9931, 2087, 11847, 8523, 2840, 1988, 5527, 5289, 2192, 3413, 1930, 2024, 3260, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 19658, 1920, 9328, 2670, 7748, 1942, 4625, 1920, 2087, 17, 9436, 8523, 4832, 3414, 1958, 3260, 5289, 18, 3], "antigen": ["KFPIYTIPDKLGPWSPIDIHHLSCPNNLVVEDEGCTNLSGFSYMELKVGYISAIKMNGFTCTGHFRPTPDACRAAYNWKMAPSVADLDPYDRSLHSPVFPGGNCSGVAVSSTYCSTNHDYTIWMPENPRLGMSCDIFTNSRGKRASKGSETCGFVDERGLYKSLKGACKLKLCGVLGLRLMDGTWVAMQTSNETKWCPPGQLVNLHDFRSDEIEPLVVEELVKKREECLDALESIMTTKSVSFRRLSHLRKLVPGFGKAYTIFNKTLMEADAHYKSVRTWNEIIPSKGCLRVGGRCHPHVNGVFFNGIILGPDGNVLIPEMQSSLLQQHMELLVSSVIPLMHPL"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human Fab (IGHV3/IGKV1-Kappa) targeting the Phosphatidylcholine translocator ABCB4 of Homo sapiens. ABCB4 is an energy-dependent phospholipid efflux translocator that translocates phosphatidylcholine from the inner to the outer leaflet of the canalicular membrane bilayer into the canaliculi of hepatocytes, protecting the biliary tree from the detergent activity of bile salts. This antibody is intended as a structural tool to stabilize distinct functional conformations of ABCB4 for structural characterization. Please generate the HCDRs for this antibody.", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVASSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFNFSSSSISSSSGSTARAYIWWYQMRQAMDY", "metadata": {"pdb_id": "7niu", "light_chain_seq": "TQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRT", "cdrh1_seq": "GFNFSSSS", "cdrh2_seq": "ISSSSGST", "cdrh3_seq": "ARAYIWWYQMRQAMDY", "cdrl1_seq": "QSVSSA", "cdrl2_seq": "SAS", "cdrl3_seq": "QQSSSSLIT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[22, 27]", "cdrl2_pos": "[45, 47]", "cdrl3_pos": "[84, 92]", "cdrh3_split": "val", "cdrh3_cluster": "7niu", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Phosphatidylcholine translocator ABCB4, Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "cryogenic electron microscopy structures of human ABCB4 in three distinct functional conformations"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 23842, 12930, 3061, 7219, 16290, 1927, 16350, 27974, 18, 7219, 16290, 1977, 1925, 3844, 17, 3100, 14608, 11247, 12930, 3061, 1988, 29102, 23842, 2037, 1920, 6671, 1942, 1920, 7642, 20097, 1927, 1920, 11152, 4588, 3260, 14269, 2460, 1920, 11152, 16058, 1033, 1927, 9919, 16, 15145, 1920, 13210, 6694, 2037, 1920, 15814, 2455, 1927, 9619, 16028, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 4493, 3183, 12526, 1927, 7219, 16290, 1958, 4346, 7285, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["TLFRYSDWQDKLFMSLGTIMAIAHGSGLPLMMIVFGEMTDKFVDTAGNFGKILEEEMTRYAYYYSGLGAGVLVAAYIQVSFWTLAAGRQIRKIRQKFFHAILRQEIGWFDINDTTELNTRLTDDISKISEGIGDKVGMFFQAVATFFAGFIVGFIRGWKLTLVIMAISPILGLSAAVWAKILSAFSDKELAAYAKAGAVAEEALGAIRTVIAFGGQNKELERYQKHLENAKEIGIKKAISANISMGIAFLLIYASYALAFWYGSTLVISKEYTIGNAMTVFFSILIGAFSVGQAAPCIDAFANARGAAYVIFDIIDNNPKIDSFSERGHKPDSIKGNLEFNDVHFSYPSRANVKILKGLNLKVQSGQTVALVGSSGCGKSTTVQLIQRLYDPDEGTINIDGQDIRNFNVNYLREIIGVVSQEPVLFSTTIAENICYGRGNVTMDEIKKAVKEANAYEFIMKLPQKFDTLVGERGAQLSGGQKQRIAIARALVRNPKILLLDEATSALDTESEAEVQAALDKAREGRTTIVIAHRLSTVRNADVIAGFEDGVIVEQGSHSELMKKEGVYFKLVNVPPVSFLKVLKLNKTEWPYFVVGTVCAIANGGLQPAFSVIFSEIIAIFGPGDDAVKQQKCNIFSLIFLFLGIISFFTFFLQGFTFGKAGEILTRRLRSMAFKAMLRQDMSWFDDHKNSTGALSTRLATDAAQVQGATGTRLALIAQNIANLGTGIIISFIYGWQLTLLLLAVVPIIAVSGIVEMKLLAGNAKRDKKELEAAGKIATEAIENIRTVVSLTQERKFESMYVEKLYGPYRNSVQKAHIYGITFSISQAFMYFSYAGCFRFGAYLIVNGHMRFRDVILVFSAIVFGAVALGHASSFAPDYAKAKLSAAHLFMLFERQPLIDSYSEEGLKPDKFEGNITFNEVVFNYPTRANVPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPLAGTVLLDGQEAKKLNVQWLRAQLGIVSQEPILFDCSIAENIAYGDNSRVVSQDEIVSAAKAANIHPFIETLPHKYETRVGDKGTQLSGGQKQRIAIARALIRQPQILLLDEATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVFQNGRVK"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A murine Fab, 2C11 (IGHV1/IGKV12-Kappa), targeting the engineered isoform 2 of Protein-serine O-palmitoleoyltransferase porcupine of Homo sapiens. Porcupine is a key regulator of the Wnt signaling pathway that mediates the attachment of palmitoleate to Wnt proteins, a modification required for efficient binding to frizzled receptors. The antibody is designed as a structural tool to enable cryo-EM visualization of native PORCN by providing a fiducial marker, with binding that does not interfere with PORCN enzymatic activity.", "target_protein": "EIQLQQSGAELVKPGASVKMSCKVSMNWVKQSHGKSLEWIGNNYNQKFTGKATFTVDRSSSTAYMQLDSLTSEDSAVYYCWGQGTLVTVSSGYSFTGYNINPYYVSTARSYGSSHTFAY", "metadata": {"pdb_id": "7urd", "light_chain_seq": "DIHMTQSPASLSAFVGETVTITCRTSENIFSYLAWYQQKQGKSPQLLVYNAKTLTSGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGSPYTFGGGTKLEIK", "cdrh1_seq": "GYSFTGYN", "cdrh2_seq": "INPYYVST", "cdrh3_seq": "ARSYGSSHTFAY", "cdrl1_seq": "ENIFSY", "cdrl2_seq": "NAK", "cdrl3_seq": "QHHYGSPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7ura", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "2C11", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV12", "is_engineered": true, "target_antigen": "Protein-serine O-palmitoleoyltransferase porcupine, Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "monoclonal antibody denoted 2C11 that explicitly binds to native PORCN...cryo-EM is challenging"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 6921, 3242, 12, 20733, 7390, 19, 7021, 1040, 7390, 1028, 17, 12093, 13, 16, 5133, 1920, 11091, 6174, 22, 1927, 2213, 17, 8468, 57, 17, 13615, 2456, 10921, 9961, 4572, 18021, 12184, 1927, 16350, 27974, 18, 4572, 18021, 12184, 1977, 43, 3834, 7888, 1927, 1920, 7028, 3197, 3374, 1988, 10412, 1920, 8576, 1927, 13615, 2456, 2010, 1942, 7028, 2697, 16, 43, 6295, 3414, 1958, 5807, 2743, 1942, 9081, 18559, 2824, 4086, 18, 1920, 3533, 1977, 4609, 1966, 43, 4346, 5229, 1942, 8675, 15822, 17, 2391, 9966, 1927, 6196, 4572, 7814, 2007, 5453, 43, 22394, 1978, 2086, 4966, 16, 1956, 2743, 1988, 3731, 2084, 11827, 1956, 4572, 7814, 8145, 2455, 18, 3], "antigen": ["FSRQEFFQQLLQGCLLPTAQQGLDQIWLLLAICLACRLLWRLGLPSYLKHASTVAGGFFSLYHFFQLHMVWVVLLSLLCYLVLFLCRHSSHRGVFLSVTILIYLLMGEMHMVDTVTWHKMRGAQMIVAMKAVSLGFDLDRGEVGTVPSPVEFMGYLYFVGTIVFGPWISFHSYLQAVQGRPLSCRWLQKVARSLALALLCLVLSTCVGPYLFPYFIPLNARWLRAYESAVSFHFSNYFVGFLSEATATLAGAGFTEEKDHLEWDLTVSKPLNVELPRSMVEVVTSWNLPMSYWLNNYVFKNALRLGTFSAVLVTYAASALLHGFSFHLAAVLLSLAFITYVEHVLRKRLARILSACVLSKRCPPDCSHQHRLGLGVRALNLLFGALAIFHLAYLGSLFDVYGMAYTVHKWSELSWASHWVTFGCWIFYRLIG"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A human Fab, MCA1 (IGHV1/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Middle East respiratory syndrome coronavirus. The Spike glycoprotein attaches the virion to the cell membrane by interacting with the host receptor DPP4 to mediate viral entry, and mediates fusion of viral and cellular membranes as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that blocks the interaction between viral S and human DPP4, binding within the BetaCoV S1-CTD.", "target_protein": "ATRLEESGAEVKKPGSSVKVSCKASISWVRQAPGQGLEWMGRNYAQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCWGQGTMVTVSSAGGTFSSYAIIPILGIAASKQGDYYDRTSYAFDI", "metadata": {"pdb_id": "5gmq", "light_chain_seq": "DVELTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPITFGQGTRLEIKRT", "cdrh1_seq": "GGTFSSYA", "cdrh2_seq": "IIPILGIA", "cdrh3_seq": "ASKQGDYYDRTSYAFDI", "cdrl1_seq": "QSVSSSY", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYGSSPIT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "5gmq", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "MCA1", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Middle East respiratory syndrome coronavirus", "target_domain": "BetaCoV S1-CTD", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody that completely inhibits MERS-CoV replication"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 2616, 6914, 16, 14035, 1009, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 5576, 10319, 5481, 4741, 5548, 10703, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 1920, 4423, 3148, 16423, 1006, 1942, 8265, 4324, 6904, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 1920, 2835, 2192, 4324, 61, 1930, 2616, 16423, 1006, 16, 2743, 2651, 1920, 4666, 4879, 1020, 4062, 17, 15898, 18, 3], "antigen": ["VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTNSVCPK"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A synthetic Fab (IGHV3/IGKV1-Kappa) targeting the pH-gated potassium channel KcsA of Streptomyces lividans. The pH-gated potassium channel KcsA acts as a pH-gated potassium ion channel; changing the cytosolic pH from 7 to 4 opens the channel. This antibody is intended as a structural tool to stabilize the channel conformation and facilitate crystallographic studies of the selectivity filter and gating mechanisms.", "target_protein": "VQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWIGENYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGYTFTSDWIIPSYGRAARERGDGYFDY", "metadata": {"pdb_id": "7mk6", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQSIGTDIHWYQQKPGKAPKLLIKYAESISGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSNRWPFTFGQGTKVEIKRT", "cdrh1_seq": "GYTFTSDW", "cdrh2_seq": "IIPSYGRA", "cdrh3_seq": "ARERGDGYFDY", "cdrl1_seq": "QSIGTD", "cdrl2_seq": "YA", "cdrl3_seq": "QQSNRWPFT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 105]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "7mdj", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "pH-gated potassium channel KcsA, Streptomyces lividans", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "Fab fragments bound in the pore mouth vicinity"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 6830, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 2087, 17, 12336, 9057, 4999, 29971, 1019, 1927, 22874, 15260, 9532, 3355, 18, 1920, 2087, 17, 12336, 9057, 4999, 29971, 1019, 8016, 1966, 43, 2087, 17, 12336, 9057, 4755, 4999, 31, 8546, 1920, 9410, 2087, 2037, 27, 1942, 24, 19851, 1920, 4999, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 1920, 4999, 7748, 1930, 6628, 17832, 2351, 1927, 1920, 9008, 6199, 1930, 12568, 3531, 18, 3], "antigen": ["CAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVVTATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALATWFVGQC"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A human Fab, p4-36 (IGHV3/IGLV2-Lambda), targeting the engineered Phosphate-binding protein PstS 1 of Mycobacterium tuberculosis H37Rv. PstS 1 is a phosphate-binding periplasmic protein that functions in inorganic phosphate uptake as part of the ABC transporter complex PstSACB and acts as a host TLR2 agonist that induces inflammatory responses and apoptosis in macrophages. The antibody is designed to restrict mycobacterial growth through Fc-dependent opsonization and antibody-mediated cellular uptake via Fc\u03b3R engagement on macrophages, conferring protection against Mycobacterium tuberculosis infection.", "target_protein": "EVQLVESGGGLVQPGRSLRLSCTDSLSWVRQAPGKGLEWVGFEYAASVKGRFTISRDDSKSVAYLQMNSLKTEDTAVYFCWGQGTLVTVSSAGFTFSEYAIRSKAYGGTTTGPRPYYDSSGYYPYYFDY", "metadata": {"pdb_id": "7dm1", "light_chain_seq": "SALTQPRSVSGSPGQSVTISCTGSRSDVGGYDYVSWYQQHPGRVPKLMIYDVTKRPSGVPDRFSGSRSGNTASLTISGLQADDEADYYCSSFAGSSTYVVFGGGTTLTVLGQ", "cdrh1_seq": "GFTFSEYA", "cdrh2_seq": "IRSKAYGGTT", "cdrh3_seq": "TGPRPYYDSSGYYPYYFDY", "cdrl1_seq": "RSDVGGYDY", "cdrl2_seq": "DVT", "cdrl3_seq": "SSFAGSSTYVV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 116]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 99]", "cdrh3_split": "val", "cdrh3_cluster": "7dm1", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "p4-36", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Phosphate-binding protein PstS 1, Mycobacterium tuberculosis H37Rv", "target_domain": null, "functional_role": "other", "evidence_quote": "mAbs p4-36 and p4-163 mediate protection in vitro and in vivo via Fc-dependent opsonization"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 2616, 6914, 16, 9068, 17, 3480, 12, 20733, 1020, 1010, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 11091, 5413, 17, 2743, 2213, 16910, 1036, 21, 1927, 16389, 8449, 29253, 24895, 18, 16910, 1036, 21, 1977, 43, 5413, 17, 2743, 24334, 2213, 1988, 4088, 1922, 13849, 5413, 5047, 1966, 3131, 1927, 1920, 7219, 9054, 2796, 16910, 5735, 18598, 1930, 8016, 1966, 43, 4423, 15235, 7829, 1988, 6387, 3769, 3387, 1930, 4091, 1922, 5205, 18, 1920, 3533, 1977, 4609, 1942, 18240, 21424, 2905, 2596, 6437, 17, 3100, 26303, 2466, 1930, 3533, 17, 3434, 3689, 5047, 3454, 17536, 1005, 9577, 1990, 5205, 16, 21510, 6202, 3316, 16389, 8449, 2909, 18, 3], "antigen": ["TVATTPASSPVTLAETGSTLLYPLFNLWGPAFHERYPNVTITAQGTGSGAGIAQAAAGTVNIGASDAYLSEGDMAAHKGLMNIALAISAQQVNYNLPGVSEHLKLNGKVLAAMYQGTIKTWDDPQIAALNPGVNLPGTAVVPLHRSDGSGDTFLFTQYLSKQDPEGWGKSPGFGTTVDFPAVPGALGENGNGGMVTGCAETPGCVAYIGISFLDQASQRGLGEAQLGNSSGNFLLPDAQSIQAAAAGFASKTPANQAISMIDGPAPDGYPIINYEYAIVNNRQKDAATAQTLQAFLHWAITDGNKASFLDQVHFQPLPPAVVKLSDALIATISS"]} {"modality_type": "antibody", "text": "Given the following functional description of an antibody, generate the HCDRs that perform the described role. The desired function is: A human Fab, S2L20 (IGHV3/IGKV1-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2, specifically the Lambda variant (C.37). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes during entry. The antibody is designed to bind the N-terminal domain (NTD) supersite as a non-neutralizing antibody, providing structural characterization of immune evasion mechanisms in the Lambda variant.", "target_protein": "EVQLVESGGGVVQPGGSLRLSCAASMHWVRQAPGKGLEWVAFYYADSVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCWGQGTLVTVSGFTFNSYGIRYDGGNKANLKDSRYSGSYYDY", "metadata": {"pdb_id": "8vyf", "light_chain_seq": "IWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKVDF", "cdrh1_seq": "GFTFNSYG", "cdrh2_seq": "IRYDGGNK", "cdrh3_seq": "ANLKDSRYSGSYYDY", "cdrl1_seq": "QDIRFY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYDNLPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "9c44", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S2L20", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "N-terminal domain (NTD)", "functional_role": "other", "evidence_quote": "NTD-targeting non-nAb"}}}, "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 16, 5655, 1920, 27203, 5675, 1988, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 5159, 11232, 1008, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 16, 4475, 1920, 18279, 6031, 12, 45, 18, 3191, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1942, 4566, 1920, 56, 17, 4262, 3418, 12, 22078, 13, 12636, 2394, 1966, 43, 2447, 17, 12130, 3533, 16, 5453, 4346, 7285, 1927, 3743, 25092, 3531, 1922, 1920, 18279, 6031, 18, 3], "antigen": ["QCVNLRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHNSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKS"]} {"modality_type": "antibody", "text": "A human Fab, F005-126 (IGHV1/IGLV1-Lambda), targeting the engineered Hemagglutinin of Influenza A virus (H3N2). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate virus attachment and entry, and undergoes low pH-induced conformational changes in endosomes to facilitate membrane fusion. The antibody is designed as a neutralizing antibody that stabilizes the HA head to prevent the low pH-induced conformational transition to the postfusion state, thereby blocking virus entry. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "QVQLVQSGAEVKKPGASVTVSCQVSLSWVRQAPGQGLEWVGWKYVKKFQGRVTMTTHTGTNTAYMEMKSLRSDDTAVYYCWGQGTMVTVSSKGYTLTSYGINTYDGQTARVEGVRGVMGFHYYPMDV", "metadata": {"pdb_id": "7k37", "light_chain_seq": "SVLTQPPSVSGAPGQRVTISCTGSSAVHWYQQLPGTAPKLLISGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSSVFGGGTKLTVLGR", "cdrh1_seq": "GYTLTSYG", "cdrh2_seq": "INTYDGQT", "cdrh3_seq": "ARVEGVRGVMGFHYYPMDV", "cdrl1_seq": "SA", "cdrl2_seq": "GNS", "cdrl3_seq": "QSSV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[24, 25]", "cdrl2_pos": "[43, 45]", "cdrl3_pos": "[82, 85]", "cdrh3_split": "val", "cdrh3_cluster": "3whe", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "F005-126", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus (strain A/Hong Kong/1/1968 H3N2)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody targeting the HA head; prevents low pH-induced conformational transition to postfusion state"}}}, "tokenized_instruction": [2, 43, 2616, 6914, 16, 17930, 15264, 17, 10483, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 11091, 26141, 1927, 7108, 43, 3413, 12, 25234, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 3413, 8576, 1930, 6904, 16, 1930, 14928, 2330, 2087, 17, 2719, 8523, 2840, 1922, 14978, 1942, 6628, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 19658, 1920, 2118, 4469, 1942, 4625, 1920, 2330, 2087, 17, 2719, 8523, 4832, 1942, 1920, 2753, 9049, 3360, 16, 6113, 7472, 3413, 6904, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["STATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEK", "GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQ"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A murine Fab, 6H1 (IGHV5/IGKV6-Kappa), targeting the Reticulocyte-binding protein 2b of Plasmodium vivax. The Reticulocyte-binding protein 2b mediates parasite invasion into human reticulocytes by binding to transferrin receptor protein 1 (TFRC). The antibody is designed as a neutralizing antibody that inhibits reticulocyte binding and blocks P. vivax invasion by targeting an inhibitory epitope on PvRBP2b.", "target_protein": "VKLVESEGGLVQPGSSMNLSCTASMAWVRQVPDKGLEWVASYYLDSLKSRFIISRDNVKNILNLQMSSLKSEDTATYYCWGQGTTLTVSSAGFTFSDYYVSYDGSITTRVTVVDSFDY", "metadata": {"pdb_id": "6bpe", "light_chain_seq": "VMTQSQKFMSTSIGVRVSVTCKASQNVGTNVAWYQQKPSPKALIYSASYRNSGVPDRFTGSGSGTEFTLTISAEYFCQQYDSYPYPFGGGTKLEIKRA", "cdrh1_seq": "GFTFSDYY", "cdrh2_seq": "VSYDGSIT", "cdrh3_seq": "TRVTVVDSFDY", "cdrl1_seq": "QNVGTN", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYDSYPYP", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 105]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[45, 47]", "cdrl3_pos": "[77, 85]", "cdrh3_split": "val", "cdrh3_cluster": "6bpe", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "6H1", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV6", "is_engineered": false, "target_antigen": "Reticulocyte-binding protein 2b, Plasmodium vivax", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "anti-PvRBP2b monoclonal antibodies inhibit reticulocyte binding and block P. vivax invasion"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 7135, 6914, 16, 16156, 1009, 12, 20733, 1020, 1015, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 18905, 4463, 17, 2743, 2213, 5751, 1927, 15663, 20236, 18, 1920, 18905, 4463, 17, 2743, 2213, 5751, 10412, 8652, 6254, 2460, 2616, 18905, 3443, 2007, 2743, 1942, 16943, 3148, 2213, 21, 12, 26817, 1030, 13, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7042, 18905, 4463, 2743, 1930, 7644, 58, 18, 20236, 6254, 2007, 5133, 1925, 5431, 10095, 1990, 24783, 19109, 1014, 18, 3], "antigen": ["TNTTDNIDYFDISDESNYYLISQLRPHFSNIYFFDEFKRYASYHTEIKRYEDIHKTKVNSLLNEASRAIGICNRAKNTVKGLINILENPQKFKTQRESYDVKLRQYEEKKEAFRGCLLNKNRKNLDQIKKINNEIRDLLEKLKCSQDCQTNVYFDMIKIYLVDFKKMPYENYDTFIKQYKNSYLSGVDMIRKIEKQIDNPVTINAIKFTQKEMGYIIDRFEYHLQKVKHSIDQVTALSDGVKPKQVTKNRLKEYYFNIGNYYSIFKFGKDSLNMLNKALIHKEKIVHNLLGELFGHLEERIS"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A human Fab, p60.12 (IGHV1/IGLV2-Lambda), targeting the Capsid protein P domain of Paslahepevirus balayani (HEV genotype 3). The antibody is designed as a glycan-sensitive neutralizing antibody that recognizes a quaternary epitope on the P domain. This antibody demonstrates broad neutralization across HEV genotypes 1\u20134 and cross-reactivity to distantly related Hepeviruses. Please provide the HCDR sequences.", "target_protein": "VQLVQSGAEVKKPGSSVKVSCKASISWVRQAPGQGLEWMGGNYAPKFQDTVTITADKSTNTVYMEMRSLRSEDTAVYYCWGQGTLVTVSSAGDTFSSYVIIPIIGTAASNVQLQRRGNWFDP", "metadata": {"pdb_id": "8pn0", "light_chain_seq": "ALTQPASVSGSPGQSITISCTGTSSDIGDYNFVSWYQQHPGKAPKLMIFDVTNRPSGVSNRFSGSKSGNTASLTISGLQVEDEADYYCSSYTSTNTPVVFGGGTKLTVLGQ", "cdrh1_seq": "GDTFSSYV", "cdrh2_seq": "IIPIIGTA", "cdrh3_seq": "ASNVQLQRRGNWFDP", "cdrl1_seq": "SSDIGDYNF", "cdrl2_seq": "DVT", "cdrl3_seq": "SSYTSTNTPVV", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 109]", "cdrl1_pos": "[23, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "8pmx", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "p60.12", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Capsid protein, Paslahepevirus balayani", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "glycan-sensitive nAb that potently neutralizes naked and quasi-enveloped HEV virions"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 2616, 6914, 16, 21139, 1008, 18, 2369, 12, 20733, 7390, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 14681, 2213, 58, 3418, 1927, 9233, 5148, 4116, 9626, 11074, 4641, 19044, 8635, 12, 19791, 5619, 23, 13, 18, 1920, 3533, 1977, 4609, 1966, 43, 15060, 17, 4532, 12130, 3533, 1988, 16197, 43, 21920, 10095, 1990, 1920, 58, 3418, 18, 2052, 3533, 7706, 4949, 14377, 3436, 19791, 7059, 21, 229, 24, 1930, 3567, 17, 8229, 1942, 29448, 2712, 3357, 9488, 5811, 1918, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["APSRPFSVLRANDVLWLSLTAAEYDQTTYGSSTNPMYVSDTVTFVNVATGAQAVARSLDWSKVTLDGRPLTTIQQYSKTFYVLPLRGKLSFWEAGTTKAGYPYNYNTTASDQILIENAAGHRVAISTYTTSLGAGPTSISAVGVLAPHSALAV", "SRPFSVLRANDVLWLSLTAAEYDQTTYGSSTNPMYVSDTVTFVNVATGAQAVARSLDWSKVTLDGRPLTTIQQYSKTFYVLPLRGKLSFWEAGTTKAGYPYNYNTTASDQILIENAAGHRVAISTYTTSLGAGPTSISAVGVLAPHSA"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human Fab (IGHV3/IGKV1-Kappa) targeting the Peptidase S1 domain of human Coagulation factor IX (des-Gla-EGF1 FIXa). Coagulation factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca\u00b2\u207a ions, phospholipids, and factor VIIIa. This antibody forms a complex with Coagulation factor IX. What would the HCDRs be?", "target_protein": "EVQLVESGGGLVQPGRSLRLSCAASMHWVRQVPGKGLEWVSGGYVDSVKGRFTISRDNAKNSLYLQMNSLRIEDTALYYCWGQGALVTVSSAGFIFDDYAISWNSDNIAKAFGSGSYYNGFDY", "metadata": {"pdb_id": "8ol9", "light_chain_seq": "DIQMTQSPSTLSASAGDRVTISCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQEYNSYIRTFGQGTKVEIKRT", "cdrh1_seq": "GFIFDDYA", "cdrh2_seq": "ISWNSDNI", "cdrh3_seq": "AKAFGSGSYYNGFDY", "cdrl1_seq": "QSISSW", "cdrl2_seq": "KAS", "cdrl3_seq": "QEYNSYIRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7ahv", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Coagulation factor IX, Homo sapiens", "target_domain": "Peptidase S1", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 24050, 4062, 3418, 1927, 2616, 12441, 2991, 13848, 12, 2270, 17, 27494, 17, 4451, 1009, 4011, 1019, 13, 18, 12441, 2991, 13848, 1977, 43, 6111, 53, 17, 3100, 3582, 2213, 1988, 17241, 1922, 1920, 7598, 3374, 1927, 2877, 12441, 2007, 15025, 2991, 66, 1942, 2496, 3500, 2386, 1922, 1920, 2990, 1927, 2332, 1189, 1323, 6982, 16, 15619, 16, 1930, 2991, 18675, 1019, 18, 2052, 3533, 4952, 43, 2796, 1956, 12441, 2991, 13848, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGRSALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKL"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A murine Fab, OXI-005 (IGHV5/IGKV19-Kappa), targeting human Insulin. Insulin decreases blood glucose concentration and increases cell permeability to monosaccharides, amino acids and fatty acids. This antibody forms a complex with the dimeric Insulin. What would the HCDRs be?", "target_protein": "EVQLVESGGGLVKPGGSLKLSCTASMSWVRQTPEKRLEWVAFYYPDTVKGRFTISRDNAENTLYLQMSSLKSEDTAIYYCWGLGTTLTVSSAGFAFSDYDISNGGYSTARQGLRYFDY", "metadata": {"pdb_id": "6z7y", "light_chain_seq": "DIQMTQSPSSLSASLGGRVTITCKASQDINKYLAWYQHKPGKGPRLLIHYTSTLQPGIPSRFSGSGSGRDYSFSISNLEPEDVATYYCLQYDSLLSFGAGTKLELKRA", "cdrh1_seq": "GFAFSDYD", "cdrh2_seq": "ISNGGYST", "cdrh3_seq": "ARQGLRYFDY", "cdrl1_seq": "QDINKY", "cdrl2_seq": "YTS", "cdrl3_seq": "LQYDSLLS", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 105]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6z7z", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "OXI-005", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV19", "is_engineered": false, "target_antigen": "Insulin, Homo sapiens", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 7135, 6914, 16, 2833, 1033, 17, 9163, 12, 20733, 1020, 1015, 19, 7021, 1040, 7390, 1026, 17, 12093, 13, 16, 5133, 2616, 4122, 18, 4122, 6386, 2877, 3817, 3110, 1930, 4041, 2024, 8828, 1942, 18491, 11926, 16, 3835, 4576, 1930, 5934, 4576, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 18150, 4122, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["NQHLCGSHLVEALYLVCGERGFFYTPKT", "GIVEQCCTSICSLYQLENYCN"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A murine Fab, 13D4 (IGHV1/IGKV6-Kappa), targeting the engineered Hemagglutinin of Influenza A virus (H5N1). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for penetration into the cell cytoplasm. The antibody is designed as a broadly neutralizing antibody targeting the receptor binding site (RBS) to prevent viral attachment and fusion. Please generate its HCDRs.", "target_protein": "VQLQQSGAELMKPGASVKISCKATIEWVKQRPGHGLEWIGEHYNEKFKGKATFAADTSSNTAYMQLSSLTSEDSAVYYCWGAGTTVTVSLAGYTFSGHWILPGSGNIARLGTTAVERDWYFDV", "metadata": {"pdb_id": "6a0z", "light_chain_seq": "DIVMTQSQKFMSASVGDRVSVTCKASQNVGTHLAWYQQKPGQSPKALIYSASYRYSGVPDRFTGSGSGTDFTLTISNVQSGDLADYFCQQYNNFPLTFGAGTKLEIKRA", "cdrh1_seq": "GYTFSGHW", "cdrh2_seq": "ILPGSGNI", "cdrh3_seq": "ARLGTTAVERDWYFDV", "cdrl1_seq": "QNVGTH", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYNNFPLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6a0z", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "13D4", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": "Receptor binding site (RBS)", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibody capable of neutralizing all representative H5N1 viruses"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 2590, 15005, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 11091, 26141, 1927, 7108, 43, 3413, 12, 20128, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 12006, 2460, 1920, 2024, 5239, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 3148, 2743, 3200, 12, 28954, 13, 1942, 4625, 4324, 8576, 1930, 5289, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["HNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYV"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab, Beta-32 (IGHV1/IGKV1-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the host cell membrane by interacting with ACE2 and other receptors, and mediates fusion of viral and cellular membranes through conformational changes. The antibody is designed as a neutralizing antibody with cross-reactive potency against multiple SARS-CoV-2 variants, engaging the right shoulder of the receptor-binding domain centered on residue 501.", "target_protein": "EVQLVQSGAEVKKPGASVKVSCKASMHWVRQAPGQGLEWMGWNYAQKFQGRVTMTRDTSITTGYMELSSLRSDDTALYYCWGQGTLVTVFSGYTFTGYYINPNSGGTARVGAHDYYDSSDNWFDP", "metadata": {"pdb_id": "7q9k", "light_chain_seq": "DIQMTQSPSSVSASVGDRLTITCRASQGISSWLAWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK", "cdrh1_seq": "GYTFTGYY", "cdrh2_seq": "INPNSGGT", "cdrh3_seq": "ARVGAHDYYDSSDNWFDP", "cdrl1_seq": "QGISSW", "cdrl2_seq": "AAS", "cdrl3_seq": "QQANSFPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 113]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "7q9k", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Beta-32", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "highly potent against all variants reported here"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 4666, 17, 3323, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 4423, 2024, 3260, 2007, 8615, 1956, 8298, 1028, 1930, 2303, 4086, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1956, 3567, 17, 6079, 10397, 3316, 3137, 20466, 17, 6083, 17, 22, 4936, 16, 15888, 1920, 3659, 12104, 1927, 1920, 3148, 17, 2743, 3418, 10841, 1990, 6181, 28397, 18, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVNCTFEYVSFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDILQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGVENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A human Fab (IGHV3/IGLV3-Lambda) targeting the H3K4me3 peptide, a synthetic construct derived from Histone H3.1. Histone H3.1 is a core component of nucleosomes and plays a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability through post-translational modifications. The antibody is designed to recognize trimethylated lysine residues on histone H3 as important epigenetic marks with exquisite specificity and high affinity for epigenetics applications.", "target_protein": "EVQLVETGGGVVQPGRSLRLSCTASMSWVRQAPGKGLEWVADYYLDAVKGRFTISRDNAKSSLYLQMNSLGAEDTAVYYCWGRGTLVTVSSAGFTFRDYWIHQDGQVRARNFVRGFGWHFDL", "metadata": {"pdb_id": "4yhz", "light_chain_seq": "LTQPPSVSVAPGQTARITCGGTNIGDISVHWYQQRPGQAPLVVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDDSINAYVFGTGTKVTVLRT", "cdrh1_seq": "GFTFRDYW", "cdrh2_seq": "IHQDGQVR", "cdrh3_seq": "ARNFVRGFGWHFDL", "cdrl1_seq": "NIGDIS", "cdrl2_seq": "DDS", "cdrl3_seq": "QVWDDSINAYV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[22, 27]", "cdrl2_pos": "[45, 47]", "cdrl3_pos": "[84, 94]", "cdrh3_split": "val", "cdrh3_cluster": "4yhz", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "H3K4me3 peptide, synthetic construct", "target_domain": null, "functional_role": "other", "evidence_quote": "antibodies to trimethylated lysine residues on histone H3, important epigenetic marks"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 28961, 1020, 1010, 17, 18279, 13, 5133, 1920, 20039, 4207, 16, 43, 6830, 6377, 3595, 2037, 6632, 8170, 18, 21, 18, 6632, 8170, 18, 21, 1977, 43, 4728, 4594, 1927, 18729, 1930, 5705, 43, 4101, 2770, 1922, 3213, 3640, 16, 2678, 5059, 16, 2678, 5158, 16, 1930, 9220, 5057, 2596, 2753, 17, 8414, 6920, 18, 1920, 3533, 1977, 4609, 1942, 9967, 21849, 1981, 9082, 4248, 1990, 6632, 8170, 1966, 2715, 8542, 13387, 1956, 1975, 17478, 4896, 1930, 2149, 5173, 1958, 30122, 5990, 18, 3], "antigen": ["ARTQTARK"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human Fab, 14B1 (IGHV3/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor, initiating infection, and mediates fusion of viral and cellular membranes through conformational changes. The antibody is designed as a broadly neutralizing antibody against SARS-CoV-2 variants, binding within the Receptor-binding domain (RBD) to sterically block ACE2 engagement. Generate the corresponding HCDRs.", "target_protein": "EVQLVESGGGVVQPGGSLRLSCVASMHWVRQTPGKGLEWVSLFYADSVQGRFTISRDNSKNSLYLQMNSLRSDDIGLYYCWGQGTMVTVSSEFTIDDYAISGDGGRTAKGGIFYNPSRFYYPNGRLVGSAFDI", "metadata": {"pdb_id": "8i3u", "light_chain_seq": "EIVMTQSPATLSVSPGERATLSCRASQNISANLAWYQQKPGQAPRLLIHGASTRATGVPGRFSGSGSGTEFTLSISSLQSEDFAVYYCQHYNNWPPLTFGGGTKVEIK", "cdrh1_seq": "EFTIDDYA", "cdrh2_seq": "ISGDGGRT", "cdrh3_seq": "AKGGIFYNPSRFYYPNGRLVGSAFDI", "cdrl1_seq": "QNISAN", "cdrl2_seq": "GAS", "cdrl3_seq": "QHYNNWPPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 121]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "8i3u", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "14B1", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "broadly and potently neutralizing mAbs...sterically disrupt the binding of human angiotensin-converting enzyme 2 (hACE2) to RBD"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 6914, 16, 2607, 5090, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 3316, 20466, 17, 6083, 17, 22, 4936, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 1942, 17638, 2169, 3367, 8298, 1028, 9577, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A human Fab, ADI-15878 (IGHV3/IGKV1-Kappa), targeting the trimeric Envelope glycoprotein of Bundibugyo ebolavirus. The Envelope glycoprotein acts as a class I viral fusion protein that mediates fusion of viral and target cell membranes during entry, and functions as a decoy for anti-GP antibodies contributing to viral immune evasion. The antibody is designed as a pan-ebolavirus broadly neutralizing antibody that targets a conserved epitope at the base of the glycoprotein.", "target_protein": "VQLVQSGVTLVQPGGSLRVSCAASMSWVRQAPGKGLEWVSAYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGALVTVSSAGFTFSSYAISGLGGSTAKDHRVWAAGYHFDY", "metadata": {"pdb_id": "6ea5", "light_chain_seq": "DIVLTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGEAPKLLISDASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYYSSPTFGGGTKVEIKRT", "cdrh1_seq": "GFTFSSYA", "cdrh2_seq": "ISGLGGST", "cdrh3_seq": "AKDHRVWAAGYHFDY", "cdrl1_seq": "QSISSW", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYYSSPT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "6dzm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ADI-15878", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Glycoprotein, Bundibugyo ebolavirus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "pan-ebolavirus neutralizing human antibody capable of potently neutralizing all five ebolaviruses"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 2616, 6914, 16, 2041, 1033, 17, 14340, 7950, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 29177, 11262, 11424, 1927, 10051, 2023, 2215, 25749, 24497, 11074, 18, 1920, 11262, 11424, 8016, 1966, 43, 2921, 51, 4324, 5289, 2213, 1988, 10412, 5289, 1927, 4324, 1930, 2758, 2024, 5726, 2409, 6904, 16, 1930, 4088, 1966, 43, 25164, 1958, 2246, 17, 4882, 3788, 8739, 1942, 4324, 3743, 25092, 18, 1920, 3533, 1977, 4609, 1966, 43, 3797, 17, 24497, 11074, 11984, 12130, 3533, 1988, 4845, 43, 5305, 10095, 2019, 1920, 5170, 1927, 1920, 11424, 18, 3], "antigen": ["AKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYTEGIMHNQNGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEP", "IPLGVVHNNTLQVSDIDKLVCRDKLSSTSQLASVGLNLEGNGVATDVPTATKRWGFRAGVPPKVVNYEAGEWAENCYNLDIKKADGSECLPEAPEGVRGFPRCRYVHKVSGTGPCPEGYAFHKEGAFFLYDRLASTIIYRSTTFSEGVVAFLILPETK"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human Fab, DJ85-c.01 (IGHV4/IGKV1-Kappa), targeting the Envelope glycoprotein gp160 of Human immunodeficiency virus 1, presented as the BG505 DS-SOSIP trimeric Env. The Envelope glycoprotein gp160 oligomerizes into trimers and is proteolytically cleaved to produce gp120 and gp41, which mediate viral attachment to host cells and membrane fusion. The antibody is designed as a broadly neutralizing antibody targeting the fusion peptide-site of vulnerability, a conserved epitope recognized by vaccine-elicited and infection-boosted fusion peptide-directed lineages capable of cross-clade neutralization. Can you generate its HCDRs?", "target_protein": "QVQLQESGPGLVKPSETLSLTCAVSWNWIRQSPGKGLEWIGNVYNPSLGSRVTFSRDTSKNQFSLRLDSVTAADTAVYFCWGQGLLVTVSAGVSISGNYYIHGNTAATATLYEFRVYMGERISYHDY", "metadata": {"pdb_id": "8tl2", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTISCRASQDISSDLNWYQQKPGKPPQLLIYFASNLQSGVPSRFSGSGAGTEFTLTINSLQAEDFASYFCLQYQSYPWTFGQGTMVDLKRT", "cdrh1_seq": "GVSISGNYY", "cdrh2_seq": "IHGNTAAT", "cdrh3_seq": "ATLYEFRVYMGERISYHDY", "cdrl1_seq": "QDISSD", "cdrl2_seq": "FAS", "cdrl3_seq": "LQYQSYPWT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 58]", "cdrh3_pos": "[97, 115]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8tl2", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DJ85-c.01", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus 1", "target_domain": "Fusion peptide-site of vulnerability", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing antibodies...fusion peptide-directed responses"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 6914, 16, 17224, 10025, 17, 45, 18, 3287, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 21, 16, 3549, 1966, 1920, 14415, 26815, 4473, 17, 17668, 2049, 29177, 11118, 18, 1920, 11262, 11424, 4882, 16954, 13034, 4517, 2460, 28220, 1930, 1977, 12712, 2169, 10246, 1942, 5074, 16102, 1930, 25618, 16, 2154, 8265, 4324, 8576, 1942, 4423, 2094, 1930, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 5289, 4207, 17, 3200, 1927, 13026, 16, 43, 5305, 10095, 6783, 2007, 5955, 17, 9856, 1930, 2909, 17, 26807, 5289, 4207, 17, 6554, 10439, 7131, 1927, 3567, 17, 11315, 14377, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLAL", "AENLWVTVYYGVPVWKDAETTLFCASDHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQIKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKR"]} {"modality_type": "antibody", "text": "Output the HCDRs for an antibody that performs this function: A human Fab (IGHV5/IGKV3-Kappa) targeting the Neuraminidase of Influenza B virus (B/Iowa/06/2017). Neuraminidase catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates. The antibody is designed to confer protection against IBV infection through dual mechanisms: direct inhibition of neuraminidase enzymatic activity and Fc-mediated effector functions including ADCC, with particular efficacy at the respiratory mucosal interface.", "target_protein": "GLQLVQSGAELKKPGESLKISCQGSIGWVRQIPGKGLEWMGIRYSPSFEGQVTISADKSVTTAYLQWSSLKASDTAMYYCWGQGTMVTVGYTFPIYWIYPGDSDTARHSEPWYPDHRFWPPYPFDI", "metadata": {"pdb_id": "8u1c", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRSSQTVSSGYLAWYQQKRGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYFCQHHGTSPGTFGGGTKVEI", "cdrh1_seq": "GYTFPIYW", "cdrh2_seq": "IYPGDSDT", "cdrh3_seq": "ARHSEPWYPDHRFWPPYPFDI", "cdrl1_seq": "QTVSSGY", "cdrl2_seq": "GAS", "cdrl3_seq": "QHHGTSPGT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 116]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "8u1c", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Neuraminidase, Influenza B virus (B/Iowa/06/2017)", "target_domain": null, "functional_role": "other", "evidence_quote": "Fc-mediated effector functions contribute to in vivo protection against IBV"}}}, "tokenized_instruction": [2, 6647, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 17436, 2052, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1015, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 29831, 1927, 7108, 44, 3413, 12, 44, 19, 22850, 19, 6604, 19, 5664, 13, 18, 29831, 17097, 1920, 6025, 1927, 4262, 20436, 2687, 4248, 2037, 4324, 1930, 3689, 4235, 30378, 2209, 18, 1920, 3533, 1977, 4609, 1942, 7909, 6202, 3316, 6180, 1020, 2909, 2596, 7064, 3531, 30, 3083, 3523, 1927, 29831, 8145, 2455, 1930, 6437, 17, 3434, 7917, 4088, 2710, 25899, 16, 1956, 3278, 4348, 2019, 1920, 5481, 9565, 6854, 18, 3], "antigen": ["PEWTYPRLSCPGSTFQKALLISPHRFLIIREPFVACGPNECKHFALTHYAARNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKVKYGEAYTDTYHSYANNILRTQESACNCIGGNCYLMITDGSASGVSECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIECACRDNRYTAKRPFVKLNVETDTAEIRLMCTDTYLDTPRPNDGSITGPCESDGDKGSGGIKGGFVHQRMKSKIGRWYSRTMSKTERMGMGLYVKYGGDPWADSDALAFSGVMVPMKEPGWYSFGFEIKDKKCDVPCIGIEMVHDHSAATAIYCLMGSGQLLWDT"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab, PGZL1.H4K3 (IGHV1/IGKV3-Kappa), targeting the membrane-proximal external region (MPER) of the Envelope glycoprotein gp160 of Human immunodeficiency virus 1. The Envelope glycoprotein gp160 oligomerizes into trimers and mediates viral attachment to host cells and membrane fusion during entry. The antibody is designed as a broadly neutralizing antibody with exceptional breadth against diverse HIV-1 primary isolates, binding within the MPER and engaging the viral membrane through lipid interactions to prevent fusion.", "target_protein": "KVQLVQSGAELKKPWSSVRVSCKASFNWVRQAPGQRLEWLGGNYAQRFRGRVTISADRSTSTVYLEMTGLTSADTAVYFCWGQGTLVTVSTAGGSFSSYAIVPLVSSTAREGEGWFGRPLRAFEF", "metadata": {"pdb_id": "6o3l", "light_chain_seq": "EIVLTQSPGTFALSPGERATLSCRASQSVSGGALAWYQQKAGQAPRLLIYGTSGRATGVPGRFSGSGSETDFSLTISRLEPEDFAVYYCQQYGTSQSTFGQGTRLETRRT", "cdrh1_seq": "GGSFSSYA", "cdrh2_seq": "IVPLVSST", "cdrh3_seq": "AREGEGWFGRPLRAFEF", "cdrl1_seq": "QSVSGGA", "cdrl2_seq": "GTS", "cdrl3_seq": "QQYGTSQST", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "6mto", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "PGZL1.H4K3", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus 1", "target_domain": "MPER; binding to GalCer", "functional_role": "neutralizing", "evidence_quote": "H4K3 neutralized 100% viruses at \u2264 50 \u03bcg/ml, with an IC 50 of 1.43 \u03bcg/ml"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 5306, 26262, 1009, 18, 27960, 1010, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 1927, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 21, 18, 1920, 11262, 11424, 4882, 16954, 13034, 4517, 2460, 28220, 1930, 10412, 4324, 8576, 1942, 4423, 2094, 1930, 3260, 5289, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1956, 24265, 22532, 3316, 6445, 3525, 17, 21, 3065, 5645, 16, 2743, 2651, 1920, 5438, 1915, 1930, 15888, 1920, 4324, 3260, 2596, 4486, 3719, 1942, 4625, 5289, 18, 3], "antigen": ["NWFDITNWLWYIKKKK"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (BA.2.75 variant). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding or proteolytic cleavage. The antibody is designed as a neutralizing antibody that remains effective against the BA.2.75 variant. Please output the HCDRs.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7yqz", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKR", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "Antibody therapeutics Evusheld and Bebtelovimab remain effective against BA.2.75"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 6813, 18, 22, 18, 4089, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 2014, 12712, 6404, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 4497, 3655, 3316, 1920, 6813, 18, 22, 18, 4089, 6031, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["TQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPVNLGRDLPQGFSALEPLVDLPIGINITRFQTLLAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFHEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPE"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A rabbit Fab, Fab92 (IGHV1/IGKV1-Kappa), targeting the engineered Fusion glycoprotein F0 of Henipavirus nipahense. The Fusion glycoprotein F0 is a class I viral fusion protein that mediates fusion of viral and cellular membranes, with conformational transitions from prefusion to postfusion states driven by heptad repeat regions that form a trimer-of-hairpins structure. The antibody is designed as a neutralizing antibody against Nipah virus infection.", "target_protein": "SLEESGGRLVTPGTPLTLTCTASMMWVRQAPGKGLEWIGIYYASWTKGRFTISKTSTTVDLKITSPTTEDTATYFCWGPGTLVTVSGFSLSSYYINTGGNAARAVPSGAGYSAGGL", "metadata": {"pdb_id": "8rvn", "light_chain_seq": "LTQTPASVEAAVGGTVTIKCQASQSVGFYLSWYQQKPGQPPKLLIYRASTLESGVPSRFKGSGSGTEFTLTISDLECADAATYYCQTNDYLASSAFGGGTEVVV", "cdrh1_seq": "GFSLSSYY", "cdrh2_seq": "INTGGNA", "cdrh3_seq": "ARAVPSGAGYSAGGL", "cdrl1_seq": "QSVGFY", "cdrl2_seq": "RAS", "cdrl3_seq": "QTNDYLASSA", "cdrh1_pos": "[23, 30]", "cdrh2_pos": "[48, 54]", "cdrh3_pos": "[91, 105]", "cdrl1_pos": "[23, 28]", "cdrl2_pos": "[46, 48]", "cdrl3_pos": "[85, 94]", "cdrh3_split": "val", "cdrh3_cluster": "8rvn", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Fab92", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Fusion glycoprotein F0, Henipavirus nipahense", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody (mAb92) that targets NiV-F to neutralize the virus"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 6020, 6914, 16, 6914, 11884, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 5289, 11424, 17930, 1927, 14618, 19514, 11074, 18786, 5945, 4480, 18, 1920, 5289, 11424, 17930, 1977, 43, 2921, 51, 4324, 5289, 2213, 1988, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 16, 1956, 8523, 10673, 2037, 9328, 2670, 1942, 2753, 9049, 4376, 6446, 2007, 20662, 2015, 6865, 3451, 1988, 2386, 43, 20085, 17, 1927, 17, 14565, 1036, 3170, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 3316, 18786, 5945, 3413, 2909, 18, 3], "antigen": ["ILHYEKLSKIGLVKGVTRKYKIKSNPLTKDIVIKMIPNVSNMSQCTGSVMENYKTRLNGILTPIKGALEIYKNNTHDGVIMAGVAIGIATAAQITAGVALYEAMKNADNINKLKSSIESTNEAVVKLQEKTVYVLTALQDYINTNLVPTIDKISCKQTELSLDLALSKYLSDLLFVFGPNLQDPVSNSMTIQAISQAFGGNYETLLRTLGYATEDFDDLLESDSITGQIIYVDLSSYYIIVRVYFPILTEIQQAYIQELLPVSFNNDNSEWISIVPNFILVRNTLISNIEIGFCLITKRSVICNQDYATPMTNNMRECLTGSTEKCPRELVVSSHVPRFALSNGVLFANCISVTCQCQTTGRAISQSGEQTLLMIDNTTCPTAVLGNVIISGKYLGSVNYNSEGIAIGPPVFTDKVDISSQISSMNQSLQQSKDYIKEA"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A human Fab, abN48-2 (IGHV1/IGLV5-Lambda), targeting a peptide from the N-terminus of C-X-C chemokine receptor type 2 (CXCR2) of Homo sapiens. CXCR2 is a receptor for interleukin-8 and other chemokines that activates neutrophils and mediates neutrophil chemotaxis to sites of tissue injury and inflammation. The antibody is designed to block IL-8-induced neutrophil chemotaxis and confer protection in autoimmune inflammatory disease models by competing with the natural IL-8 ligand for binding to the CXCR2 N-terminus, thereby inhibiting neutrophil migration and inducing CXCR2 internalization.", "target_protein": "QVQLVQSGAEVKKPGSSVKVSCKASISWVRQAPGQGPEWMGWNYAQKFQGRVTMTRDTSISTAYMELSRLRPDDTAVYYCWGQGTLVTVSSAGGTLSSYAINPNSGGTASGYCSRTRCYDY", "metadata": {"pdb_id": "6kva", "light_chain_seq": "VLTQPSSLSASPGASVSLTCTLRSGINVGAYRIYWYQQKPGSPPQFLLRYKSDSDKQQGSGVPSRFSGSRDASANAGILLISGLRSEDEADYYCAIWHSSAWVFGGGTQLTVLGG", "cdrh1_seq": "GGTLSSYA", "cdrh2_seq": "INPNSGGT", "cdrh3_seq": "ASGYCSRTRCYDY", "cdrl1_seq": "SGINVGAYR", "cdrl2_seq": "YKSDSDK", "cdrl3_seq": "AIWHSSAWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[23, 31]", "cdrl2_pos": "[49, 55]", "cdrl3_pos": "[94, 102]", "cdrh3_split": "val", "cdrh3_cluster": "6kvf", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "abN48-2", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV5", "is_engineered": false, "target_antigen": "C-X-C chemokine receptor type 2, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "blocks neutrophil chemotaxis and protects mice in an EAE model"}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 4456, 6301, 17, 22, 12, 20733, 7390, 19, 28961, 1020, 1015, 17, 18279, 13, 16, 5133, 43, 4207, 2037, 1920, 56, 17, 7822, 1927, 45, 17, 66, 17, 45, 11673, 3148, 2601, 22, 12, 30353, 13, 1927, 16350, 27974, 18, 30353, 1977, 43, 3148, 1958, 9198, 17, 28, 1930, 2303, 12370, 1988, 9094, 8508, 1930, 10412, 9460, 16884, 1942, 3402, 1927, 2960, 4047, 1930, 4531, 18, 1920, 3533, 1977, 4609, 1942, 3367, 2614, 17, 28, 17, 2719, 9460, 16884, 1930, 7909, 6202, 1922, 8904, 3769, 2573, 3130, 2007, 11743, 1956, 1920, 4613, 2614, 17, 28, 5207, 1958, 2743, 1942, 1920, 30353, 56, 17, 7822, 16, 6113, 7918, 9460, 5049, 1930, 7834, 30353, 12071, 18, 3], "antigen": ["FEDFWKG"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human single-chain Fv (scFv), pT1511 (IGHV3/IGKV2-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors including ACE2, TFRC, GRM2, NRP1/NRP2, integrin, and ASGR1, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. This antibody forms a complex with the Spike glycoprotein within the BetaCoV S1-CTD.", "target_protein": "EVQLVESGGALVQPGRSLRLSCAASMHWVRQAPGKGLEWVSGGYADSVKGRFTISRDNAKNSLYLQVNSLRAEDTALYYCWGQGTLVTVSSAGFTFDDYAIDWNSGSIVKDSRAHYDILATYVGFDY", "metadata": {"pdb_id": "8bg1", "light_chain_seq": "IVMTQFPLSLPVTPGEPASISCRSSQSLLHSNGNNYLDWYLQKPGQSPQLLIYLNSNRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQALQTPTFGQGTRLEIKRT", "cdrh1_seq": "GFTFDDYA", "cdrh2_seq": "IDWNSGSI", "cdrh3_seq": "VKDSRAHYDILATYVGFDY", "cdrl1_seq": "QSLLHSNGNNY", "cdrl2_seq": "LNS", "cdrl3_seq": "MQALQTPT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[25, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 99]", "cdrh3_split": "val", "cdrh3_cluster": "8bg1", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "scFv", "heavy_subclass": "IGHV3", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "BetaCoV S1-CTD", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 2957, 17, 4659, 11417, 12, 19863, 13, 16, 4401, 23375, 1009, 12, 20733, 1020, 1010, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 2710, 8298, 1028, 16, 26817, 1030, 16, 2398, 8224, 16, 5214, 5113, 19, 5214, 5991, 16, 8920, 16, 1930, 1966, 2299, 1009, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 11424, 2651, 1920, 4666, 4879, 1020, 4062, 17, 15898, 18, 3], "antigen": ["NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPD"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab, Ofatumumab (IGHV3/IGKV3-Kappa), targeting the B-lymphocyte antigen CD20 of Homo sapiens. CD20 is a B-lymphocyte-specific membrane protein that plays a role in the regulation of cellular calcium influx necessary for the development, differentiation, and activation of B-lymphocytes, functioning as a store-operated calcium channel component. The antibody is designed as a type I therapeutic antibody that promotes complement activation through optimal geometry for complement recruitment.", "target_protein": "EVQLVESGGGLVQPGRSLRLSCAASMHWVRQAPGKGLEWVSTGYADSVKGRFTISRDNAKKSLYLQMNSLRAEDTALYYCWGQGTTVTVSSAGFTFNDYAISWNSGSIAKDIQYGNYYYGMDV", "metadata": {"pdb_id": "6y92", "light_chain_seq": "EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPITFGQGTRLEIKRT", "cdrh1_seq": "GFTFNDYA", "cdrh2_seq": "ISWNSGSI", "cdrh3_seq": "AKDIQYGNYYYGMDV", "cdrl1_seq": "QSVSSY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQRSNWPIT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "6y92", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Ofatumumab", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "B-lymphocyte antigen CD20, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "type I mAb complexes act as molecular seeds to increase mAb local concentration for efficient complement activation"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 1927, 9576, 6683, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 44, 17, 10009, 4730, 16494, 1927, 16350, 27974, 18, 16494, 1977, 43, 44, 17, 10009, 17, 2487, 3260, 2213, 1988, 5705, 43, 2770, 1922, 1920, 3640, 1927, 3689, 5016, 12403, 4680, 1958, 1920, 2740, 16, 4155, 16, 1930, 2936, 1927, 44, 17, 7257, 16, 7295, 1966, 43, 14582, 17, 10497, 5016, 4999, 4594, 18, 1920, 3533, 1977, 4609, 1966, 43, 2601, 51, 4272, 3533, 1988, 7383, 5508, 2936, 2596, 5419, 10869, 1958, 5508, 6067, 18, 3], "antigen": ["TQSFFMRESKTLGAVQIMNGLFHIALGGLLMIPAGIYAPICVTVWYPLWGGIMYIISGSLLAATEKNSRKCLVKGKMIMNSLSLFAAISGMILSIMDILNIKISHFLKMESLNFIRAHTPYINIYNCEPANPSEKNSPSTQYCYSIQSLFLGILSVMLIFAFFQELVIAGIVENEWKR"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A human Fab, F005-126 (IGHV1/IGLV1-Lambda), targeting the engineered Hemagglutinin of Influenza A virus (strain A/Hong Kong/1/1968 H3N2). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and undergoes low pH-induced conformational changes in endosomes to facilitate membrane fusion. The antibody is designed as a neutralizing antibody that stabilizes the HA head to prevent the low pH-induced transition to the postfusion state, thereby blocking the conformational changes required for viral membrane fusion.", "target_protein": "QVQLVQSGAEVKKPGASVTVSCQVSLSWVRQAPGQGLEWVGWKYVKKFQGRVTMTTHTGTNTAYMEMKSLRSDDTAVYYCWGQGTMVTVSSKGYTLTSYGINTYDGQTARVEGVRGVMGFHYYPMDV", "metadata": {"pdb_id": "7k3a", "light_chain_seq": "SVLTQPPSVSGAPGQRVTISCTGSSAVHWYQQLPGTAPKLLISGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSSVFGGGTKLTVLGR", "cdrh1_seq": "GYTLTSYG", "cdrh2_seq": "INTYDGQT", "cdrh3_seq": "ARVEGVRGVMGFHYYPMDV", "cdrl1_seq": "SA", "cdrl2_seq": "GNS", "cdrl3_seq": "QSSV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[24, 25]", "cdrl2_pos": "[43, 45]", "cdrl3_pos": "[82, 85]", "cdrh3_split": "val", "cdrh3_cluster": "3whe", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "F005-126", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus (strain A/Hong Kong/1/1968 H3N2)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody targeting the HA head; prevents low pH-induced conformational transition to postfusion state"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 2616, 6914, 16, 17930, 15264, 17, 10483, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 11091, 26141, 1927, 7108, 43, 3413, 12, 3943, 43, 19, 15908, 18143, 19, 21, 19, 22553, 25234, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 14928, 2330, 2087, 17, 2719, 8523, 2840, 1922, 14978, 1942, 6628, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 19658, 1920, 2118, 4469, 1942, 4625, 1920, 2330, 2087, 17, 2719, 4832, 1942, 1920, 2753, 9049, 3360, 16, 6113, 7472, 1920, 8523, 2840, 3414, 1958, 4324, 3260, 5289, 18, 3], "antigen": ["STATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEK", "GFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQ"]} {"modality_type": "antibody", "text": "Here is the antibody function: A rhesus macaque Fab, GPZ6-b.01 (IGHV4/IGKV1-Kappa), targeting the Envelope glycoprotein gp160 of Human immunodeficiency virus 1. The Envelope glycoprotein gp160 oligomerizes into trimers and is proteolytically cleaved to produce gp120 and gp41, which mediate viral attachment and membrane fusion during entry. The antibody is designed as a neutralizing antibody targeting the fusion peptide-site of vulnerability, binding within this conserved epitope region to achieve broad cross-clade neutralization. Generate the corresponding HCDRs.", "target_protein": "QVQLQESGPGLVKPSETLSLTCAVYWHWIRQAPGKGLEWIGDGYNPSLKRRVRISADTSKNQFSLNLRSVTAADTAVYFCWGAGVLVTVGSSISGGYFYVYFSGTTARDPRGGGWVPNRFDV", "metadata": {"pdb_id": "8top", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQDISSFLNWYQQKPGKAPKLLISSVNRLESGVPSRFSGSGSGTEFTLTVSSLQPEDFATYSCQQCGSVPYTFGQGTTL", "cdrh1_seq": "GSSISGGYFY", "cdrh2_seq": "VYFSGTT", "cdrh3_seq": "ARDPRGGGWVPNRFDV", "cdrl1_seq": "QDISSF", "cdrl2_seq": "SVN", "cdrl3_seq": "QQCGSVPYT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8top", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "GPZ6-b.01", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus 1", "target_domain": "Fusion peptide-site of vulnerability", "functional_role": "neutralizing", "evidence_quote": "GPZ6-b.01 recognize the fusion peptide-site of vulnerability with ~35-45% breadth on a 208-strain panel"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 16996, 20533, 6914, 16, 4882, 1011, 1016, 17, 44, 18, 3287, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 21, 18, 1920, 11262, 11424, 4882, 16954, 13034, 4517, 2460, 28220, 1930, 1977, 12712, 2169, 10246, 1942, 5074, 16102, 1930, 25618, 16, 2154, 8265, 4324, 8576, 1930, 3260, 5289, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 5289, 4207, 17, 3200, 1927, 13026, 16, 2743, 2651, 2052, 5305, 10095, 3031, 1942, 6230, 4949, 3567, 17, 11315, 14377, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["AVFLGFLGAAGSTMGAASMTLTVQARNLLSTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLAL", "AENLWVTVYYGVPVWKDAETTLFCASDHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQIKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRR"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human Fab, DL11 (IGHV3/IGKV1-Kappa), targeting the engineered extracellular region (domains I\u2013III) of Receptor tyrosine-protein kinase erbB-3 (HER3). HER3 is a tyrosine-protein kinase that plays an essential role as a cell surface receptor for neuregulins, binding neuregulin-1 and activating phosphatidylinositol 3-kinase signaling. The antibody is designed as part of a dual-specificity approach to inhibit both HER3 and EGFR-mediated signaling in cancer. Can you generate its HCDRs?", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWLGEDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTLSGDWISAAGGYTARESRVSFEAAMDY", "metadata": {"pdb_id": "3p11", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQDLATDVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSEPEPYTFGQGTKVEIKRT", "cdrh1_seq": "GFTLSGDW", "cdrh2_seq": "ISAAGGYT", "cdrh3_seq": "ARESRVSFEAAMDY", "cdrl1_seq": "QDLATD", "cdrl2_seq": "SAS", "cdrl3_seq": "QQSEPEPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3p11", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DL11", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Receptor tyrosine-protein kinase erbB-3, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "dual HER3/EGFR specificity with superior inhibitory activity compared with monospecific antibodies"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 6914, 16, 5268, 3242, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 5329, 3031, 12, 4682, 51, 229, 4337, 13, 1927, 3148, 6941, 17, 2213, 4016, 11954, 17, 23, 12, 3656, 1010, 13, 18, 3656, 1010, 1977, 43, 6941, 17, 2213, 4016, 1988, 5705, 1925, 4415, 2770, 1966, 43, 2024, 3154, 3148, 1958, 2974, 6541, 19962, 16, 2743, 2974, 6541, 3392, 17, 21, 1930, 8019, 16927, 23, 17, 4016, 3197, 18, 1920, 3533, 1977, 4609, 1966, 3131, 1927, 43, 7064, 17, 4896, 2998, 1942, 2875, 2321, 3656, 1010, 1930, 5775, 17, 3434, 3197, 1922, 2539, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["AVCPGTLNGLSVTGDAENQYQTLYKLYERCEVVMGNLEIVLTGHNADLSFLQWIREVTGYVLVAMNEFSTLPLPNLRVVRGTQVYDGKFAIFVMLNYNTNSSHALRQLRLTQLTEILSGGVYIEKNDKLCHMDTIDWRDIVRDRDAEIVVKDNGRSCPPCHEVCKGRCWGPGSEDCQTLTKTICAPQCNGHCFGPNPNQCCHDECAGGCSGPQDTDCFACRHFNDSGACVPRCPQPLVYNKLTFQLEPNPHTKYQYGGVCVASCPHNFVVDQTSCVRACPPDKMEVDKNGLKMCEPCGGLCPKACEGTGSGSRFQTVDSSNIDGFVNCTKILGNLDFLITGLNGDPWHKIPALDPEKLNVFRTVREITGYLNIQSWPPHMHNFSVFSNLTTIGGRSLYNRGFSLLIMKNLNVTSLGFRSLKEISAGRIYISANRQLCYHHSLNWTKVLRGPTEERLDIKHNRPRRDCVAEGKVCDPLCSSGGCWGPGPGQCLSCRNYSRGGVCVTH"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A murine Fab (IGHV1/IGKV2-Kappa), FL-1061, targeting the engineered Hemagglutinin of Influenza A virus (strain A/Aichi/2/1968 H3N2). Hemagglutinin binds to sialic acid-containing receptors on the cell surface to mediate viral attachment and entry, and functions as a class I viral fusion protein responsible for membrane fusion in the endosome. This antibody forms a complex with Hemagglutinin.", "target_protein": "EVQLQESGAELVMPGASVKLSCKASMHWVKQRPGQGLEWIGEYYNQKFKGKSTLTVDKSSSTAYMQLNSLTSEDSAVYYCWGTGTTVTVGASGYTFTRYWIDPSDSYTARNYGSSYGYFDV", "metadata": {"pdb_id": "8g5b", "light_chain_seq": "DIVMTQAAFSNPVTLGTSASISCRSSKSLLHSNGITYLYWYLQRPGQSPQLLIYQMSNLASGVPDRFSSSGSGTDFTLRISRVEAEDVGVYYCAQNLELPWTFGGGTKLEIK", "cdrh1_seq": "GYTFTRYW", "cdrh2_seq": "IDPSDSYT", "cdrh3_seq": "ARNYGSSYGYFDV", "cdrl1_seq": "KSLLHSNGITY", "cdrl2_seq": "QMS", "cdrl3_seq": "AQNLELPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "8g5b", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV2", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 2300, 17, 7758, 1009, 16, 5133, 1920, 11091, 26141, 1927, 7108, 43, 3413, 12, 3943, 43, 19, 14765, 7969, 19, 22, 19, 22553, 25234, 13, 18, 26141, 6876, 1942, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 4324, 8576, 1930, 6904, 16, 1930, 4088, 1966, 43, 2921, 51, 4324, 5289, 2213, 5061, 1958, 3260, 5289, 1922, 1920, 22321, 18, 2052, 3533, 4952, 43, 2796, 1956, 26141, 18, 3], "antigen": ["ELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGIHHPSTDQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVK"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human Fab, 3A6 (IGHV3/IGKV2-Kappa), targeting the GP2 epitope peptide derived from the Envelope glycoprotein of Zaire ebolavirus (strain Eckron-76). The Envelope glycoprotein mediates viral entry through trimeric GP1,2 complexes on the virion surface, with GP2 functioning as the membrane fusion subunit. This antibody forms a complex with the GP2 epitope peptide. Please generate the HCDRs for this antibody.", "target_protein": "EVQLLESGGGLVKPGGSLRLSCAASMNWVRQPPGKGLEWVSSNYADSVKGRFTISRDNAKNSLYLQMNSLRSDDTAMYYCWGQGTLITVSSAGFTFNEYMISGTSTYIARGSTGGY", "metadata": {"pdb_id": "7rpu", "light_chain_seq": "DIVMTQTPLSSAVTLGQPASISCRSSQRLVHSDGNTYLSWLHQRPGQPPRLLIYKVSLRFSGVPDRFSGSGAGTDFTLKISRVEAEDVGIYYCMQATQFPLTFGGGTKVEIKRT", "cdrh1_seq": "GFTFNEYM", "cdrh2_seq": "ISGTSTYI", "cdrh3_seq": "ARGSTGGY", "cdrl1_seq": "QRLVHSDGNTY", "cdrl2_seq": "KVS", "cdrl3_seq": "MQATQFPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 103]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "7rpu", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "3A6", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "GP2 epitope peptide, Zaire ebolavirus (strain Eckron-76)", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 5694, 1016, 12, 20733, 1020, 1010, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 4882, 1028, 10095, 4207, 3595, 2037, 1920, 11262, 11424, 1927, 26112, 2952, 24497, 11074, 12, 3943, 3270, 21783, 1916, 17, 5439, 13, 18, 1920, 11262, 11424, 10412, 4324, 6904, 2596, 29177, 4882, 1009, 16, 22, 5048, 1990, 1920, 19230, 3154, 16, 1956, 4882, 1028, 7295, 1966, 1920, 3260, 5289, 5903, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 4882, 1028, 10095, 4207, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["IHDFVDKTLPDQG"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human Fab, Tocilizumab (IGHV4/IGKV1-Kappa), targeting the Interleukin-6 receptor subunit alpha (IL-6R). IL-6R binds interleukin-6 with low affinity and, upon association with IL6ST, transduces signals that regulate immune response, acute-phase reactions, and hematopoiesis; classic signaling through membrane-bound IL-6R is regenerative and anti-inflammatory. The antibody is designed to inhibit IL-6 signaling by blocking the IL-6 binding site on IL-6R, preventing IL-6/IL-6R/gp130 complex formation.", "target_protein": "QVQLQESGPGLVRPSQTLSLTCTVSWSWVRQPPGRGLEWIGYTYNPSLKSRVTMLRDTSKNQFSLRLSSVTAADTAVYYCWGQGSLVTVSSAGYSITSDHAISYSGITARSLARTTAMDY", "metadata": {"pdb_id": "8j6f", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQDISSYLNWYQQKPGKAPKLLIYYTSRLHSGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQGNTLPYTFGQGTKVEIKRT", "cdrh1_seq": "GYSITSDHA", "cdrh2_seq": "ISYSGIT", "cdrh3_seq": "ARSLARTTAMDY", "cdrl1_seq": "QDISSY", "cdrl2_seq": "YTS", "cdrl3_seq": "QQGNTLPYT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8j6f", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Tocilizumab", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Interleukin-6 receptor subunit alpha, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "inhibit IL-6/IL-6R signaling by competing for the IL-6 binding site"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 6914, 16, 21682, 5912, 19240, 3368, 1014, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 9198, 17, 26, 3148, 5903, 4595, 12, 2614, 17, 29680, 13, 18, 2614, 17, 29680, 6876, 9198, 17, 26, 1956, 2330, 5173, 1930, 16, 4073, 3279, 1956, 19610, 2156, 16, 30334, 1036, 4771, 1988, 5741, 3743, 2644, 16, 3939, 17, 3193, 5298, 16, 1930, 21941, 31, 12211, 3197, 2596, 3260, 17, 4124, 2614, 17, 29680, 1977, 15310, 1930, 2246, 17, 3769, 18, 1920, 3533, 1977, 4609, 1942, 2875, 2614, 17, 26, 3197, 2007, 7472, 1920, 2614, 17, 26, 2743, 3200, 1990, 2614, 17, 29680, 16, 8444, 2614, 17, 26, 19, 2614, 17, 29680, 19, 4882, 12285, 2796, 3337, 18, 3], "antigen": ["QPDPPANITVVTWQDPHSWNSSFYRLRFELRYRATWMVKDLQHHHVVQLRAQEEFGQGEWSEWSPE", "FRKSPLSNVV"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A murine Fab (IGHV5/IGKV4-Kappa) targeting the Type-2 angiotensin II receptor of Homo sapiens. The Type-2 angiotensin II receptor is a G protein-coupled receptor that signals via non-canonical pathways and cooperates with MTUS1 to inhibit ERK2 activation and cell proliferation. This antibody is intended as a structural tool to stabilize the receptor for crystallographic characterization of ligand-bound conformational states. What would the HCDRs be?", "target_protein": "DVQLVESGGGLVQPGGSRKLSCAASMHWVRQAPEKGLEWVAYYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTAMYFCWGQGTLVTVSAAGFTFSGFGISSGSSLIATSLYYGTPWFAY", "metadata": {"pdb_id": "6jod", "light_chain_seq": "DIVLTQSPAIMSASPGEKVTMTCSASSSVTYMYWYQQKPGSSPRLLIYDTSNLASGVPVRFSGSGSGTSYSLTISRMEAEDAATFYCQQWSSYPLTFGAGTKLELKRA", "cdrh1_seq": "GFTFSGFG", "cdrh2_seq": "ISSGSSLI", "cdrh3_seq": "ATSLYYGTPWFAY", "cdrl1_seq": "SSVTY", "cdrl2_seq": "DTS", "cdrl3_seq": "QQWSSYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 108]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "5xjm", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Type-2 angiotensin II receptor, Homo sapiens", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "solved the crystal structure of human AT2R bound to AngII and its specific antibody"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 7135, 6914, 12, 20733, 1020, 1015, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1920, 2601, 17, 22, 10814, 2890, 3148, 1927, 16350, 27974, 18, 1920, 2601, 17, 22, 10814, 2890, 3148, 1977, 43, 49, 2213, 17, 6416, 3148, 1988, 4771, 3454, 2447, 17, 9452, 3873, 1930, 23230, 1036, 1956, 4638, 1957, 1009, 1942, 2875, 23979, 2936, 1930, 2024, 4031, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 1920, 3148, 1958, 17832, 7285, 1927, 5207, 17, 4124, 8523, 4376, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["CSQKPSDKHLDAIPILYYIIFVIGFLVNIVVVTLFCCQKGPKKVSSIYIFNLAVADLLLLATLPLWATYYSYRYDWLFGPVMCKVFGSFLTLNMFASIFFITCMSVDRYQSVIYPFLSQRRNPWQASYIVPLVWCMACLSSLPTFYFRDVRTIEYLGVNACIMAFPPEKYAQWAAGIALMKNILGFIIPLIFIATCYFGIRKHLLKTNSYGKNRITRDQVLKMAAAVVLAFIICWLPFHVLTFLDALAWMGVINSCEVIAVIDLALPFAILLGFTNSCVNPFLYCFVGNRFQQKLRSVFRVPITWL", "ETLNDNLKVIEKADNAAQVKDALTKMRAAALDILVGQIDDALKLANEGKVKEAQAAAEQ"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab, Ab803 (IGHV3/IGKV1-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding and proteolytic cleavage. The antibody is designed as a neutralizing antibody with broad activity against multiple SARS-CoV-2 variants including BA.1 and BA.2 Omicron strains.", "target_protein": "VQLVESGGGLVQPGRSLRVSCAASMHWVRQTPRKGLEWVAGAYADSVKGRFTISRDNAKNSVFLQMNGLRADDTALYYCWGRGTLVTVSGFTFDDYAISRNSAAIVKSPRYGWGSPDYSFDF", "metadata": {"pdb_id": "7y6n", "light_chain_seq": "IQLTQSPSSLSASVGDRVTITCRASQNIGTYLNWYQQEPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYCCQQSFTTPLTFGQGTKVEIK", "cdrh1_seq": "GFTFDDYA", "cdrh2_seq": "ISRNSAAI", "cdrh3_seq": "VKSPRYGWGSPDYSFDF", "cdrl1_seq": "QNIGTY", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSFTTPLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 111]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "7y6n", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Ab803", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "Ab803 can neutralize the BA.1 and BA.2 strains"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 2186, 4476, 1010, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 1930, 12712, 6404, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1956, 4949, 2455, 3316, 3137, 20466, 17, 6083, 17, 22, 4936, 2710, 6813, 18, 21, 1930, 6813, 18, 22, 7254, 1935, 2830, 4046, 18, 3], "antigen": ["NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab, D48 (IGHV3/IGKV1-Kappa), targeting the Envelope glycoprotein B of Human herpesvirus 1 (strain KOS). Envelope glycoprotein B forms spikes at the surface of the virion envelope, binds to host cell entry receptors MYH9/NMMHC-IIA and MYH10/NMMHC-IIB, and mediates fusion of viral and cellular membranes during virus entry. The antibody is designed as a neutralizing antibody against HSV-1.", "target_protein": "EVQLVETGGGVVRPGRSLRLSCTTSMHWVRQAPGKGLEWVAVQYHDSVKGRFTISRDNSKNVLLLQMNSLRVDDTAMYYCWGQGTMVTVSSGFSFSGSAISHDGNIIARDVWLLPATISYAFDF", "metadata": {"pdb_id": "8kfa", "light_chain_seq": "VIWMTQSPPSLSASIGDTVTITCRASQGISNSIAWYQRRPGKAPELLVYAAYRLQSGVPSRLSGSGSGAEYTLTIKNMQPEDFATYYCQQYYDNPLTFGGGTKVEIK", "cdrh1_seq": "GFSFSGSA", "cdrh2_seq": "ISHDGNII", "cdrh3_seq": "ARDVWLLPATISYAFDF", "cdrl1_seq": "QGISNS", "cdrl2_seq": "AAY", "cdrl3_seq": "QQYYDNPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8kfa", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "D48", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein B, Human herpesvirus 1 (strain KOS)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 16, 16603, 1025, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 44, 1927, 2616, 25718, 21, 12, 3943, 23818, 13, 18, 11262, 11424, 44, 4952, 14533, 2019, 1920, 3154, 1927, 1920, 19230, 11262, 16, 6876, 1942, 4423, 2024, 6904, 4086, 27242, 1026, 19, 2943, 22316, 1030, 17, 17433, 1930, 27242, 2930, 19, 2943, 22316, 1030, 17, 19795, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2409, 3413, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 3316, 10681, 17, 21, 18, 3], "antigen": ["ANFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTTYAADRFKQVDGFYARDLAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYQANGGFLIAYQPLLSNTVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRVAIAWCELQNHELTLWNEARKLNPNAIASVTVGRRVSARMLGDVMAVSTCVPVAADNVIVQNSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIHA"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptor ACE2, initiating infection, and mediates fusion of the virion and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting the Receptor-binding domain (RBD), and does not compete with DARPin SR22 or antibody CR3022 for binding.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "8dw2", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "anti-SARS-CoV-2 antibody Fabs, S309 and CR3022"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 3148, 8298, 1028, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 1920, 19230, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 1930, 3731, 2084, 17269, 1956, 14574, 9512, 4581, 4460, 2014, 3533, 2345, 29906, 1028, 1958, 2743, 18, 3], "antigen": ["LCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG"]} {"modality_type": "antibody", "text": "Here is the antibody function: A human Fab, DH511.2 (IGHV3/IGKV1-Kappa), targeting the membrane-proximal external region (MPER) of HIV-1 gp41. The gp41 MPER is part of the envelope glycoprotein that mediates fusion of viral and host cell membranes during entry. The antibody is designed as a broadly neutralizing antibody targeting the distal MPER, recognizing a transiently exposed intermediate conformation of gp41 that is induced after CD4-mediated Env activation, binding within the MPER domain. Generate the corresponding HCDRs.", "target_protein": "QVQLVQSGGGLVKPGGSLTLSCSASMGWVRQAPGKGLEWVGREYGAAVKDRFTISRDDSRNMLYLHMRTLKTEDSGTYYCWGRGTTVIVSSAGFFFDNSWIRRLKDGATGTMDEGTPVTRFLEWGYFYYYMAV", "metadata": {"pdb_id": "5u3l", "light_chain_seq": "DIVMTQSPSSVSASVGDRVTITCRASQNIRDYLNWYQHKPGGSPRLLIYAASTLQTGVPSRFSGSGSGNLFTLTITNLQPEDFATYYCQENYNTIPSLSFGQGTKVDIRRT", "cdrh1_seq": "GFFFDNSW", "cdrh2_seq": "IRRLKDGATG", "cdrh3_seq": "TMDEGTPVTRFLEWGYFYYYMAV", "cdrl1_seq": "QNIRDY", "cdrl2_seq": "AAS", "cdrl3_seq": "QENYNTIPSLS", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 120]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "5u3m", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DH511.2", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "gp41 MPER peptide, Human immunodeficiency virus 1", "target_domain": "MPER; binding to GalCer", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing distal MPER bnAbs...neutralized 206 of 208 viruses (99%)"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3533, 2347, 30, 43, 2616, 6914, 16, 6781, 7912, 1009, 18, 22, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 1927, 3525, 17, 21, 25618, 18, 1920, 25618, 5438, 1915, 1977, 3131, 1927, 1920, 11262, 11424, 1988, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 6583, 5438, 1915, 16, 15667, 43, 12145, 4616, 6129, 7748, 1927, 25618, 1988, 1977, 2719, 2256, 4095, 17, 3434, 11118, 2936, 16, 2743, 2651, 1920, 5438, 1915, 3418, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["KKKWNWFDITNWLWYIRKK"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A murine Fab, 22D11 (IGHV2/IGKV3-Kappa), targeting the E2 AS412 peptide of Hepatitis C virus. The E2 glycoprotein mediates virus attachment to the host cell and participates in virion internalization and fusion with the host membrane. The antibody is designed as a broadly neutralizing antibody that recognizes the conserved antigenic site AS412 in a \u03b2-hairpin conformation and cross-neutralizes diverse HCV genotypes. Please output the HCDRs.", "target_protein": "EVQLLESGPGLVAPSQSLSITCTVSVHWVRQPPGKGLEWLGANYNSALMSRLSISRDNSKSQVFLKMNSLQTDDTAMYYCWGQGTLVTVSAAGFSLTSYGIWSAGNTACAPIYYDYTWFAY", "metadata": {"pdb_id": "6bzy", "light_chain_seq": "EIVLTQSPASLAVSLGQRATISCRASESVDNYGISFMNWFQQKPGQPPKLLIYAASNQGSGVPARFSGSGSGTDFSLNIHPMEEDDTAMYFCQQSKEVPYTFGGGTKLEIKRA", "cdrh1_seq": "GFSLTSYG", "cdrh2_seq": "IWSAGNT", "cdrh3_seq": "ACAPIYYDYTWFAY", "cdrl1_seq": "ESVDNYGISF", "cdrl2_seq": "AAS", "cdrl3_seq": "QQSKEVPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 108]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "6bzy", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "22D11", "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "E2 AS412 peptide, Hepatitis C virus", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "cross-neutralize diverse HCV genotypes"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 2950, 7240, 1009, 12, 20733, 15755, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 6602, 1966, 8099, 1028, 4207, 1927, 7977, 45, 3413, 18, 1920, 6602, 11424, 10412, 3413, 8576, 1942, 1920, 4423, 2024, 1930, 17241, 1922, 19230, 12071, 1930, 5289, 1956, 1920, 4423, 3260, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1988, 16197, 1920, 5305, 14606, 3200, 1966, 8099, 1028, 1922, 43, 161, 17, 14565, 7748, 1930, 3567, 17, 25885, 1036, 6445, 6749, 7059, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["QLINTNGSWHI"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A murine Fab, 19B5 (IGHV10/IGKV6-Kappa), targeting the Calcium release-activated calcium channel protein 1 (Orai) of Drosophila melanogaster. Orai is the pore-forming subunit of hexameric CRAC channels that mediate store-operated Ca\u00b2\u207a entry upon endoplasmic reticulum Ca\u00b2\u207a depletion and channel activation by the Ca\u00b2\u207a sensor Stim. The antibody is designed as a structural tool, serving as a fiducial marker to increase particle mass and enable accurate orientation determination in cryo-EM reconstruction, binding to the extracellular side of the channel at the M1\u2013M2 loop without inhibiting channel function.", "target_protein": "VQLVESGGGLVQPKGSLKLSCAASMHWVRQAPKGLEWVARYYADSVKDRFTISRDDSQSMLYLQMNNLKTEDTAMYYCWGQGTTLTVSSAGFTFNTYAIRTNYATVRQKYGNYFDY", "metadata": {"pdb_id": "7kr5", "light_chain_seq": "VVMTQSQKFMSTSVGDRVSVTCKASQNVGINVAWYQQKPGQSPKALINSASYRNSGVPDRFTGGGSGTDFTLTINNVQSEDLAEYFCQQCNSYPLTFGAGTKLELRRA", "cdrh1_seq": "GFTFNTYA", "cdrh2_seq": "IRTNYAT", "cdrh3_seq": "VRQKYGNYFDY", "cdrl1_seq": "QNVGIN", "cdrl2_seq": "SAS", "cdrl3_seq": "QQCNSYPLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[48, 54]", "cdrh3_pos": "[93, 103]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "7kr5", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "19B5", "antibody_format": "Fab", "heavy_subclass": "IGHV10", "light_subclass": "IGKV6", "is_engineered": false, "target_antigen": "Calcium release-activated calcium channel protein 1, Drosophila melanogaster", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "fiducial-assisted cryo-electron microscopy; monoclonal Fab antibody fragments that increase mass and serve as fiducial markers"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 2282, 24462, 12, 20733, 7390, 1008, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 5133, 1920, 5016, 4012, 17, 4128, 5016, 4999, 2213, 21, 12, 23591, 13, 1927, 8273, 15572, 18, 23591, 1977, 1920, 8554, 17, 7402, 5903, 1927, 25602, 1935, 24422, 1030, 5628, 1988, 8265, 14582, 17, 10497, 2332, 1189, 1323, 6904, 4073, 13355, 12279, 2332, 1189, 1323, 6882, 1930, 4999, 2936, 2007, 1920, 2332, 1189, 1323, 6443, 2801, 18, 1920, 3533, 1977, 4609, 1966, 43, 4346, 5229, 16, 13915, 1966, 43, 22394, 1978, 2086, 4966, 1942, 2760, 7022, 3411, 1930, 8675, 6305, 7148, 7063, 1922, 15822, 17, 2391, 7101, 16, 2743, 1942, 1920, 5329, 4159, 1927, 1920, 4999, 2019, 1920, 8510, 229, 6056, 5881, 2979, 7918, 4999, 2347, 18, 3], "antigen": ["AKLKASSKTSALLSGFAMVAMVEVQLDHDTNVPPGMLIAFAICTTLLVAVAMLALMISTCILHWYIETAWAFSTLLGLILFLLEIAILCWVKFYDLSPPAAWSATVVLIPVMIIFMAFAIHFYRSLV"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A murine Fab (IGHV1/IGKV12-Kappa), Fab1A1, targeting Myomaker of Ciona robusta. Myomaker is a skeletal muscle-specific membrane protein essential for myoblast fusion, containing seven transmembrane helices that adopt a G-protein-coupled receptor-like fold. This antibody is intended as a structural tool for cryo-EM studies of the dimeric Myomaker complex. Please provide the HCDR sequences.", "target_protein": "QAYLQQSGAELVRPGASVKMSCKASMHWVKQTPRQGLEWIGASNNQKFKGKATLTVDKSSNTAYMQLSSLTSEDSAVYFCWGQGTLVTVSSGYTFTSYNIYPGNGESARGEGNYFRSGWFAY", "metadata": {"pdb_id": "8t05", "light_chain_seq": "DIVMTQSPASLSVPVGETVTITCRTSENIYSNLAWYQQKQGKSPQLLVYAATNLADGVPSRFSGSGSGTQYSLKINSLQSEDFGSYYCQHFWSTPWTFGEGTKLEIK", "cdrh1_seq": "GYTFTSYN", "cdrh2_seq": "IYPGNGES", "cdrh3_seq": "ARGEGNYFRSGWFAY", "cdrl1_seq": "ENIYSN", "cdrl2_seq": "AAT", "cdrl3_seq": "QHFWSTPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8t05", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV12", "is_engineered": false, "target_antigen": "Myomaker, Ciona robusta", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "Cryo-EM structures of Myomaker reveal a molecular basis for myoblast fusion"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 1028, 17, 12093, 13, 16, 6914, 15527, 16, 5133, 15924, 3368, 13548, 1927, 3371, 12502, 5786, 1019, 18, 15924, 3368, 13548, 1977, 43, 7345, 3760, 17, 2487, 3260, 2213, 4415, 1958, 30188, 5289, 16, 3165, 5260, 9117, 12789, 1988, 14103, 43, 49, 17, 2213, 17, 6416, 3148, 17, 3189, 3728, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1958, 15822, 17, 2391, 2351, 1927, 1920, 18150, 15924, 3368, 13548, 2796, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["GLILVKFLLPAISSGAFFIPGIFATKKRLFTLAFLYIFTAFFQLFFHLCTTPLLSLLFCLMGKKLLTFFSTYGLVLSIYSTLTQLTRYTDDRKHSAVVCGGLLIGVRIFQENEGPGVYAGPLITGGLLLAISWGQEMYRSKALYPDKEKWLKIILPSFALGAVSLLLLCVFQNSWNYAFVHSIHHLLMSAAITIILRLVED"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human antibody (IGHV1/IGKV3-Kappa) targeting the engineered Spike protein S2 of Severe acute respiratory syndrome coronavirus 2. The S2 subunit mediates fusion of the virion and cellular membranes by functioning as a class I viral fusion protein and drives viral entry. The antibody is designed as a structural tool to stabilize and visualize the pre-fusion conformation of S2, which is metastable and prone to irreversible collapse into the post-fusion state.", "target_protein": "QVQLVQSGAEVRKPGASVKVSCKASIHWVRQAPGQGLEWMGWNYAQKFQGWVIMTRDTSISTAYMELSRLTSDDTAVYYCWGQGTVVTVGYTFTGYYINPNSGGTARCGARSYYYDSGDYCAFDI", "metadata": {"pdb_id": "8v5v", "light_chain_seq": "IRMTQSPSTLSVSPGERATLSCRASQSVSSYLAWYQHKPGQAPRLLVYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNWPPPFTFGPGTKVD", "cdrh1_seq": "GYTFTGYY", "cdrh2_seq": "INPNSGGT", "cdrh3_seq": "ARCGARSYYYDSGDYCAFDI", "cdrl1_seq": "QSVSSY", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYNNWPPPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 97]", "cdrh3_split": "val", "cdrh3_cluster": "8v5v", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "antibody", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike protein S2, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "One mAb was used to solve a high-resolution cryo-EM structure of pre-fusion S2"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 3533, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 11091, 10429, 2213, 5159, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 5159, 5903, 10412, 5289, 1927, 1920, 19230, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 1930, 15435, 4324, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 4346, 5229, 1942, 13448, 1930, 13159, 1920, 2097, 17, 5289, 7748, 1927, 5159, 16, 2154, 1977, 4025, 2115, 1930, 10424, 1942, 14104, 15687, 2460, 1920, 2753, 17, 5289, 3360, 18, 3], "antigen": ["ACSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQCYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSCLLAGTICSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFK"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A murine Fab, DTA-1 (IGHV5), targeting an engineered fusion construct of Tumor necrosis factor receptor superfamily member 18 with Enhanced green fluorescent protein (N- to C-terminus). Tumor necrosis factor receptor superfamily member 18 is a receptor for TNFSF18 involved in interactions between activated T-lymphocytes and endothelial cells and in the regulation of T-cell receptor-mediated cell death. The antibody is designed as an agonist that mimics the endogenous ligand by clustering dimeric mGITR to activate NF-\u03baB signaling; optimal agonistic activity requires the divalent IgG format to bridge and cluster receptor dimers into extended arrays.", "target_protein": "LQLVESGGGLVQPGRSLKLSCSASMAWVRQAPKKGLEWVATYYPDSVKGRFTISRDTAKSSLYLQMNSLKSEDTATYYCWGQGVMVTVSSAGFIFSNSYINPSGSRTARHDLSFDY", "metadata": {"pdb_id": "7rfp", "light_chain_seq": "QFTLTQPKSVSGSLRSTITIPCDRSSGGIRDSYVSWYQQHLGRPPLNVIYADDQRPSEVSDRFSGSIDSSSNSASLTITNLQMDDEADYFCQSYDSDFDVYIFGGGTKLTVLGQ", "cdrh1_seq": "GFIFSNSY", "cdrh2_seq": "INPSGSRT", "cdrh3_seq": "ARHDLSFDY", "cdrl1_seq": "SGGIRDSY", "cdrl2_seq": "ADD", "cdrl3_seq": "QSYDSDFDVYI", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 103]", "cdrl1_pos": "[25, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[91, 101]", "cdrh3_split": "val", "cdrh3_cluster": "7rfp", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DTA-1", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": null, "is_engineered": true, "target_antigen": "Tumor necrosis factor receptor superfamily member 18 fused to Enhanced green fluorescent protein, Mus musculus", "target_domain": null, "functional_role": "other", "evidence_quote": "agonistic antibody DTA-1 IgG can cluster purified mGITR dimers; DTA-1 and TRX518 must be in an IgG form to drive optimal signaling of GITR"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 7135, 6914, 16, 7711, 1019, 17, 21, 12, 20733, 1020, 1015, 13, 16, 5133, 1925, 11091, 5289, 6377, 1927, 2798, 7476, 2991, 3148, 13975, 7210, 2654, 1956, 4256, 4524, 6265, 2213, 12, 56, 17, 1942, 45, 17, 7822, 13, 18, 2798, 7476, 2991, 3148, 13975, 7210, 2654, 1977, 43, 3148, 1958, 4705, 1036, 5739, 1025, 3286, 1922, 3719, 2192, 4128, 62, 17, 7257, 1930, 5003, 2094, 1930, 1922, 1920, 3640, 1927, 62, 17, 2024, 3148, 17, 3434, 2024, 3539, 18, 1920, 3533, 1977, 4609, 1966, 1925, 7829, 1988, 14679, 1920, 5355, 5207, 2007, 7616, 18150, 2786, 4250, 1942, 6980, 4651, 17, 6389, 3197, 31, 5419, 30350, 2455, 5474, 1920, 21610, 5166, 10387, 1942, 11925, 1930, 4377, 3148, 13351, 2460, 6091, 10517, 18, 3], "antigen": ["CGPGKVQNGSGNNTRCCSLYAPGKEDCPKERCICVTPEYHCGDPQCKICKHYPCQPGQRVESQGDIVFGFRCVACAMGTFSAGRDGHCRLWTNCSQFGFLTMFPGNKTHNAVCIPEPL"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab, E2-RecA (IGHV1/IGKV3-Kappa), targeting the engineered extracellular domain of ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 (CD38) of Homo sapiens. CD38 is a multifunctional transmembrane glycoprotein that synthesizes second messengers for calcium mobilization and signal transduction, functions as a receptor for lymphocyte activation, and regulates dendritic cell maturation. The antibody is designed as part of a biparatopic bispecific format (ISB 1442) to engage non-overlapping epitopes on CD38 and enable trans binding to adjacent CD38 molecules on tumor cell surfaces, enhancing Fc-mediated effector functions including ADCC, ADCP, and CDC for treatment of hematological malignancies.", "target_protein": "QVQLVQSGAEVKKPGSSVKVSCKASIGWVRQAPGQGLEWMGRHYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCWGQGTLVTVSSAGLPDATYAIIPRLDAEARGLGYYLYSSYYFDI", "metadata": {"pdb_id": "9goy", "light_chain_seq": "EIVMTQSPATLSVSPGERATLSCRASQSVSSNLAWYQQKPGQAPRLLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNWPWTFGQGTKVEIKRT", "cdrh1_seq": "GLPDATYA", "cdrh2_seq": "IIPRLDAE", "cdrh3_seq": "ARGLGYYLYSSYYFDI", "cdrl1_seq": "QSVSSN", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYNNWPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9goy", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "biparatopic bispecific antibody to reestablish synthetic immunity in CD38+ hematological malignancies"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 16, 6602, 17, 21534, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 5329, 3418, 1927, 9828, 17, 29117, 2199, 16526, 19, 9821, 9828, 17, 17870, 20748, 21, 12, 21274, 13, 1927, 16350, 27974, 18, 21274, 1977, 43, 20136, 9117, 11424, 1988, 15541, 1036, 2812, 16716, 1036, 1958, 5016, 14586, 1930, 2733, 8201, 16, 4088, 1966, 43, 3148, 1958, 10009, 2936, 16, 1930, 7014, 8104, 2024, 7655, 18, 1920, 3533, 1977, 4609, 1966, 3131, 1927, 43, 8446, 9041, 27747, 1935, 7266, 10231, 10387, 12, 1977, 1014, 12851, 1028, 13, 1942, 11580, 2447, 17, 8984, 11427, 1990, 21274, 1930, 8675, 2127, 2743, 1942, 6811, 21274, 4206, 1990, 2798, 2024, 7553, 16, 9221, 6437, 17, 3434, 7917, 4088, 2710, 25899, 16, 14219, 1034, 16, 1930, 7137, 1958, 2311, 1927, 17339, 10672, 18, 3], "antigen": ["WRQQWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFATSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKN"]} {"modality_type": "antibody", "text": "Generate the HCDR sequences given the following functional description of an antibody. The desired function is: A human Fab, COVA2-15 (IGHV3/IGKV2-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody targeting the receptor-binding domain in the down conformation, capable of engaging all three RBD domains of the trimeric spike.", "target_protein": "QVQLLESGGGLVQPGGSLRLSCAASMSWVRQAPGKGLEWASAYYADSVEGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCWGQGTLVTVSSGFTFSSYAISGSGGSTAKDTGYCGDDCYIKLIRGGPDY", "metadata": {"pdb_id": "9aru", "light_chain_seq": "DIVMTQSPLSLPVTLGQPASISCRSSQSLVYSDGNTFLNWFQQRPGQSPRRLIYQVSNRDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQGTHWPRTFGQGTKLEI", "cdrh1_seq": "GFTFSSYA", "cdrh2_seq": "ISGSGGST", "cdrh3_seq": "AKDTGYCGDDCYIKLIRGGPDY", "cdrl1_seq": "QSLVYSDGNTF", "cdrl2_seq": "QVS", "cdrl3_seq": "MQGTHWPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 117]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "9b82", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "COVA2-15", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV2", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "COVA2-15 with very high neutralization potency"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 3709, 3258, 1920, 2894, 3183, 8418, 1927, 1925, 3533, 18, 1920, 9465, 2347, 1977, 30, 43, 2616, 6914, 16, 6083, 8398, 17, 2461, 12, 20733, 1020, 1010, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 3148, 17, 2743, 3418, 1922, 1920, 3292, 7748, 16, 7131, 1927, 15888, 2136, 2559, 25780, 4682, 1927, 1920, 29177, 10429, 18, 3], "antigen": ["QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTETWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSCAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTICSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes during entry. The antibody is designed as a neutralizing antibody binding within the Receptor-binding domain (RBD), with the objective of maintaining recognition across divergent Omicron variants despite convergent RBD mutations. Can you generate its HCDRs?", "target_protein": "VQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "8s9g", "light_chain_seq": "IVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKV", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 114]", "cdrl1_pos": "[25, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 95]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "S309 neutralizing antibody; sotrovimab protects against BQ.1.1 and XBB.1.5"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 16, 1956, 1920, 4470, 1927, 8231, 5708, 3436, 13609, 7254, 1935, 2830, 4936, 4281, 18489, 25780, 3527, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["NLCPFHEVFNATTFASVYAWNRTRISNCVADYSVLYNFAFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGFNCYSPLQSYGFRPTYGVGHQPYRVVVLSFEVCG"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to these antibody design specifications: A human Fab (IGHV1/IGKV6-Kappa), one of three antibodies in a cocktail complex, targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding and proteolytic cleavage. This antibody forms a complex with the Spike glycoprotein as part of a multi-antibody cocktail designed to engage the trimeric spike through multiple mechanisms.", "target_protein": "QLVQSGAEVKKPGATVKISCKVSIHWVKQAPGKSLEWIGYSDNLKFKGAATLTADTSTDTAYMELSSLRSEDTAVYYCWGQGTTVTVSSAGYSFSNYYIDPFNGGTARSEYDPYYVMDY", "metadata": {"pdb_id": "7e5r", "light_chain_seq": "IVLTQSPFQSVSPKEKVTITCRASQSISSNLHWYQQKPDQSPKLLIKYASQSISGIPSRFSGSGSGTDFTLTINSLEAEDFGIYFCQQTNFWPYIFGQGTKLEIL", "cdrh1_seq": "GYSFSNYY", "cdrh2_seq": "IDPFNGGT", "cdrh3_seq": "ARSEYDPYYVMDY", "cdrl1_seq": "QSISSN", "cdrl2_seq": "YAS", "cdrl3_seq": "QQTNFWPYI", "cdrh1_pos": "[23, 30]", "cdrh2_pos": "[48, 55]", "cdrh3_pos": "[94, 106]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 94]", "cdrh3_split": "val", "cdrh3_cluster": "7cak", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2144, 3533, 3036, 22437, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 25606, 17, 12093, 13, 16, 2340, 1927, 2559, 3788, 1922, 43, 12719, 2796, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 1930, 12712, 6404, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 11424, 1966, 3131, 1927, 43, 2779, 17, 3533, 12719, 4609, 1942, 11580, 1920, 29177, 10429, 2596, 3137, 3531, 18, 3], "antigen": ["QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human IgG (IGHV2/IGLV2-Lambda), LY-CoV1404, targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors, initiating infection, and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding. The antibody is designed as a broadly neutralizing antibody with activity against multiple SARS-CoV-2 variants, binding within the Receptor-binding domain (RBD). Please output the HCDRs.", "target_protein": "ITLKESGPTLVKPTQTLTLTCTFSVGWLRQPPGKALEWLALRYSPSLKSRLTISKDTSKNQVVLKMTNIDPVDTATYYCWGQGTLVTVSSAGFSLSISGVGIYWDDDKAHHSISTIFDH", "metadata": {"pdb_id": "7mmo", "light_chain_seq": "SALTQPASVSGSPGQSITISCTATSSDVGDYNYVSWYQQHPGKAPKLMIFEVSDRPSGISNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTTSSAVFGGGTKLTVLGR", "cdrh1_seq": "GFSLSISGVG", "cdrh2_seq": "IYWDDDK", "cdrh3_seq": "AHHSISTIFDH", "cdrl1_seq": "SSDVGDYNY", "cdrl2_seq": "EVS", "cdrl3_seq": "SSYTTSSAV", "cdrh1_pos": "[24, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "7mmo", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "LY-CoV1404", "antibody_format": "IgG", "heavy_subclass": "IGHV2", "light_subclass": "IGLV2", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "potently neutralizes SARS-CoV-2 authentic virus and known variants of concern"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 5166, 12, 20733, 15755, 19, 28961, 15755, 17, 18279, 13, 16, 7518, 17, 6083, 14482, 1006, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 1956, 2455, 3316, 3137, 20466, 17, 6083, 17, 22, 4936, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A murine Fab, 4C1 (IGHV3/IGKV14-Kappa), targeting the Der p 1 allergen of Dermatophagoides pteronyssinus. Der p 1 is a cysteine protease that cleaves and activates the host G protein-coupled receptor MRGPRX1 and elicits IgE responses in allergic subjects. The antibody is designed to recognize a cross-reactive epitope on group 1 house dust mite allergens associated with IgE recognition, targeting surface-exposed residues that are molecular targets for allergen vaccine development.", "target_protein": "EVQLQESGPGLVKPSQSLSLTCTVTWNWIRQFPGNKLEWMGYSYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCWGQGTLVTVSAAGYSITSDYAISYSGTTGRTGVYRYPERAPY", "metadata": {"pdb_id": "5vpg", "light_chain_seq": "QIVMTQSPFSMYATLGERVTITCKASQDIYSYLSWLQQKPGKSLKTLIYRANRLITGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPYTFGGGTKLEMKRA", "cdrh1_seq": "GYSITSDYA", "cdrh2_seq": "ISYSGTT", "cdrh3_seq": "GRTGVYRYPERAPY", "cdrl1_seq": "QDIYSY", "cdrl2_seq": "RAN", "cdrl3_seq": "LQYDEFPYT", "cdrh1_pos": "[25, 33]", "cdrh2_pos": "[51, 57]", "cdrh3_pos": "[96, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5vpl", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV14", "is_engineered": false, "target_antigen": "Der p 1 allergen (Peptidase 1), Dermatophagoides pteronyssinus", "target_domain": null, "functional_role": "other", "evidence_quote": "binds to a unique cross-reactive epitope on both allergens associated with IgE recognition"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 7135, 6914, 16, 8235, 1009, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 1006, 17, 12093, 13, 16, 5133, 1920, 3135, 58, 21, 15468, 1927, 13467, 4965, 12363, 19147, 14186, 5590, 22214, 18, 3135, 58, 21, 1977, 43, 8666, 7154, 1988, 23839, 1930, 9094, 1920, 4423, 49, 2213, 17, 6416, 3148, 2852, 19874, 1005, 7653, 1930, 21809, 10777, 3387, 1922, 10519, 3297, 18, 1920, 3533, 1977, 4609, 1942, 9967, 43, 3567, 17, 6079, 10095, 1990, 2210, 21, 5953, 14677, 24688, 19226, 2458, 1956, 10777, 5708, 16, 5133, 3154, 17, 4616, 4248, 1988, 2032, 3272, 4845, 1958, 15468, 5955, 2740, 18, 3], "antigen": ["TNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNANKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A human Fab, DH1317.8 (IGHV7/IGKV1-Kappa), targeting the Envelope glycoprotein gp160 of Human immunodeficiency virus 1, specifically the membrane-proximal external region (MPER) peptide. The Envelope glycoprotein gp160 attaches the virus to the host lymphoid cell by binding to the primary receptor CD4, inducing structural rearrangement that creates a high-affinity binding site for chemokine coreceptors. The antibody is designed as a neutralizing antibody targeting the MPER, a conserved epitope class for broadly neutralizing antibodies against HIV-1. Please generate its HCDRs.", "target_protein": "QVQLVQSGSELKKPGASVKVSCEASITWVRQAPGQGLEWMAWTSAQGFTGRFVFSLGTSVNTTYLQIRSLRAEDTAVYYCWGTGSMVTVSSAGYTFTDYAINTNTGNPARLRRGGYNNYYMDV", "metadata": {"pdb_id": "8g8a", "light_chain_seq": "DIQMTQSPSSVSASVGDRVTITCRASQGISNWLAWYQQKPGKAPSLLIYGTSTLHRGVPSRFSGSGSGTDFTLTISSLHPEDVATYYCQQTNSFPPKWPFGQGTKVEIKRT", "cdrh1_seq": "GYTFTDYA", "cdrh2_seq": "INTNTGNP", "cdrh3_seq": "ARLRRGGYNNYYMDV", "cdrl1_seq": "QGISNW", "cdrl2_seq": "GTS", "cdrl3_seq": "QQTNSFPPKWP", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "8g8a", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DH1317.8", "antibody_format": "Fab", "heavy_subclass": "IGHV7", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus 1", "target_domain": "MPER", "functional_role": "neutralizing", "evidence_quote": "MPER peptide-liposome induction of polyclonal HIV-1 B cell lineages of mature bnAbs"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6781, 22977, 1027, 18, 28, 12, 20733, 1020, 1027, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 21, 16, 4475, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 4207, 18, 1920, 11262, 11424, 4882, 16954, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1988, 15628, 43, 2149, 17, 5173, 2743, 3200, 1958, 11673, 30435, 3448, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 1920, 5438, 1915, 16, 43, 5305, 10095, 2921, 1958, 11984, 12130, 3788, 3316, 3525, 17, 21, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["KNEQELLELDKWAS"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A human Fab (IGHV1/IGLV3-Lambda), Fab 8066, targeting the Gp41 helix of Human Immunodeficiency Virus 1. The Gp41 helix is the retroviral envelope protein that mediates fusion of viral and host cell membranes during entry. The antibody is designed as a broadly neutralizing antibody targeting the conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR), capable of engaging the trimeric N-HR structure with high affinity while maintaining neutralization activity against diverse HIV-1 subtypes.", "target_protein": "QLVQSGAEVKKPGSSVKVSCKASFSWVRQAPGQGLEWMGSNYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCWGQGTLVTVSSAGGTFNSYAIIPIFGTTARYFDTYNNYGFAN", "metadata": {"pdb_id": "4kht", "light_chain_seq": "IELTQPPSVSVVPGQTARISCSGDNIPYEYASWYQQKPGQAPVLVIYGDNNRPSGIPERFSGSNSGNTATLTISGTQAEDEADYYCASWDSMTVDGVFGGGTKLTVLGQ", "cdrh1_seq": "GGTFNSYA", "cdrh2_seq": "IIPIFGTT", "cdrh3_seq": "ARYFDTYNNYGFAN", "cdrl1_seq": "NIPYEY", "cdrl2_seq": "GDN", "cdrl3_seq": "ASWDSMTVDGV", "cdrh1_pos": "[23, 30]", "cdrh2_pos": "[48, 55]", "cdrh3_pos": "[94, 107]", "cdrl1_pos": "[24, 29]", "cdrl2_pos": "[47, 49]", "cdrl3_pos": "[86, 96]", "cdrh3_split": "val", "cdrh3_cluster": "4khx", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV3", "is_engineered": false, "target_antigen": "Gp41 helix, Human Immunodeficiency Virus 1", "target_domain": "Retroviral envelope protein GP41-like", "functional_role": "neutralizing", "evidence_quote": "Fab 8066 broadly neutralizing across a wide panel of HIV-1 subtype B and C viruses"}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 28961, 1020, 1010, 17, 18279, 13, 16, 6914, 3729, 7283, 16, 5133, 1920, 25618, 7864, 1927, 2616, 13141, 3413, 21, 18, 1920, 25618, 7864, 1977, 1920, 16599, 11262, 2213, 1988, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 5305, 4495, 29177, 17524, 17, 9121, 1927, 1920, 56, 17, 20662, 2015, 6865, 12, 56, 17, 3668, 13, 16, 7131, 1927, 15888, 1920, 29177, 56, 17, 3668, 3170, 1956, 2149, 5173, 2679, 8231, 14377, 2455, 3316, 6445, 3525, 17, 21, 8160, 18, 3], "antigen": ["CCGGIKKEIEAIKKEQEAIKKKIEAIEKELSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARIL"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A human Fab, F005-126 (IGHV1/IGLV1-Lambda), targeting the engineered Hemagglutinin of Influenza A virus (strain A/Hong Kong/1/1968 H3N2). Hemagglutinin binds sialic acid-containing receptors on the cell surface to mediate virus attachment and entry, and undergoes low pH-induced conformational changes in endosomes to facilitate membrane fusion. The antibody is designed as a neutralizing antibody that stabilizes the HA head to prevent the low pH-induced transition to the postfusion state, thereby blocking virus entry.", "target_protein": "QVQLVQSGAEVKKPGASVTVSCQVSLSWVRQAPGQGLEWVGWKYVKKFQGRVTMTTHTGTNTAYMEMKSLRSDDTAVYYCWGQGTMVTVSSKGYTLTSYGINTYDGQTARVEGVRGVMGFHYYPMDV", "metadata": {"pdb_id": "7k3b", "light_chain_seq": "SVLTQPPSVSGAPGQRVTISCTGSSAVHWYQQLPGTAPKLLISGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSSVFGGGTKLTVLGR", "cdrh1_seq": "GYTLTSYG", "cdrh2_seq": "INTYDGQT", "cdrh3_seq": "ARVEGVRGVMGFHYYPMDV", "cdrl1_seq": "SA", "cdrl2_seq": "GNS", "cdrl3_seq": "QSSV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 114]", "cdrl1_pos": "[24, 25]", "cdrl2_pos": "[43, 45]", "cdrl3_pos": "[82, 85]", "cdrh3_split": "val", "cdrh3_cluster": "3whe", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "F005-126", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV1", "is_engineered": true, "target_antigen": "Hemagglutinin, Influenza A virus (strain A/Hong Kong/1/1968 H3N2)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody targeting the HA head; prevents low pH-induced conformational transition to postfusion state"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 2616, 6914, 16, 17930, 15264, 17, 10483, 12, 20733, 7390, 19, 28961, 7390, 17, 18279, 13, 16, 5133, 1920, 11091, 26141, 1927, 7108, 43, 3413, 12, 3943, 43, 19, 15908, 18143, 19, 21, 19, 22553, 25234, 13, 18, 26141, 6876, 20436, 2687, 17, 3165, 4086, 1990, 1920, 2024, 3154, 1942, 8265, 3413, 8576, 1930, 6904, 16, 1930, 14928, 2330, 2087, 17, 2719, 8523, 2840, 1922, 14978, 1942, 6628, 3260, 5289, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 19658, 1920, 2118, 4469, 1942, 4625, 1920, 2330, 2087, 17, 2719, 4832, 1942, 1920, 2753, 9049, 3360, 16, 6113, 7472, 3413, 6904, 18, 3], "antigen": ["HAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVP", "NGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQ"]} {"modality_type": "antibody", "text": "Here is the functional description of an antibody I want to create: A human Fab, Z2B3 (IGHV1/IGLV2-Lambda), targeting the Neuraminidase of Influenza A virus (H1N1, A/Brevig Mission/1/1918 strain). Neuraminidase catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates, cleaving sialic acids during virus budding and spread to facilitate efficient progeny virus release and cell-to-cell transmission. The antibody is designed as a neutralizing antibody with cross-reactivity to both group 1 (N1) and group 2 (N9) neuraminidases, binding within the conserved active site of the Head of neuraminidase to inhibit sialidase activity and confer protection against seasonal and avian influenza strains. Please provide the HCDR sequences.", "target_protein": "EVQLVQSGAEVKKPGSSVKVSCKASFSWVRQAPGQGLEWMGGNYAQKFQGRVTITADESTSTAYMELSSLKSEDTAVYYCWGQGTTVTVSSAGGPFSSYGIIPVYGTTARDLQDTPMVDRIIGSYYYYNGLDV", "metadata": {"pdb_id": "6lxi", "light_chain_seq": "SVLTQPASVSGSPGQSITISCTGASSDVGDYNYVSWYQQHPGKAPKLMIYDVSNRPSGVSNRFSGSKSGDTASLTISGLQAEDEADYYCSSYTRSSSVVFGGGTKLTVLGQ", "cdrh1_seq": "GGPFSSYG", "cdrh2_seq": "IIPVYGTT", "cdrh3_seq": "ARDLQDTPMVDRIIGSYYYYNGLDV", "cdrl1_seq": "SSDVGDYNY", "cdrl2_seq": "DVS", "cdrl3_seq": "SSYTRSSSVV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 120]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "6lxj", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Z2B3", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Neuraminidase, Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)", "target_domain": "Head of neuraminidase", "functional_role": "neutralizing", "evidence_quote": "cross-reactivity to both N9 and broad range of seasonal and avian N1 proteins; restored binding and inhibition; regain protection against variant influenza strain"}}}, "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 1925, 3533, 51, 12914, 1942, 7762, 30, 43, 2616, 6914, 16, 68, 9385, 1010, 12, 20733, 7390, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 29831, 1927, 7108, 43, 3413, 12, 15355, 16, 43, 19, 3022, 2165, 1029, 23073, 19, 21, 19, 18162, 1025, 3943, 13, 18, 29831, 17097, 1920, 6025, 1927, 4262, 20436, 2687, 4248, 2037, 4324, 1930, 3689, 4235, 30378, 2209, 16, 28634, 20436, 4576, 2409, 3413, 15909, 1930, 6441, 1942, 6628, 5807, 13743, 3413, 4012, 1930, 2024, 17, 1942, 17, 2024, 5303, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1956, 3567, 17, 8229, 1942, 2321, 2210, 21, 12, 13007, 13, 1930, 2210, 22, 12, 56, 1026, 13, 29831, 1036, 16, 2743, 2651, 1920, 5305, 3500, 3200, 1927, 1920, 4469, 1927, 29831, 1942, 2875, 12952, 9200, 2455, 1930, 7909, 6202, 3316, 10995, 1930, 14529, 7108, 4046, 18, 11586, 3394, 1920, 27203, 1005, 3709, 18, 3], "antigen": ["VILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTIMTDGPSNGQASYKILKIEKGKVTKSIELNAPNYHYEECSCYPDTGKVMCVCRDNWHGSNRPWVSFDQNLDYQIGYICSGVFGDNPRPNDGTGSCGPVSSNGANGIKGFSFRYDNGVWIGRTKSTSSRSGFEMIWDPNGWTETDSSFSVRQDIVAITDWSGYSGSFVQHPELTGLDCMRPCFWVELIRGQPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFSIDK"]} {"modality_type": "antibody", "text": "Please generate the HCDR sequences for an antibody with the following role: A rabbit Fab (IGHV1/IGKV1-Kappa) targeting the engineered Glycoprotein of Rift valley fever virus. The Glycoprotein is a structural component of the virion that attaches to the host cell receptor CD209/DC-SIGN and promotes fusion of membranes with the late endosome after endocytosis, while shielding the hydrophobic fusion loops of glycoprotein C. The antibody is designed as a neutralizing antibody targeting domain B of the Gn glycoprotein, which is under immune-mediated selective pressure and represents an immunodominant region among phleboviruses.", "target_protein": "TGSLEESGGRLVTPGTPLTLTCTVSMSWVRQAPGKGLEWIAIYYASWAKGRFTISKTSTTVDLRIASPTTEDTATYFCWGQGTLVTVSGTGIDPNSDHIYASGTTATYPNYPTDNL", "metadata": {"pdb_id": "6i9i", "light_chain_seq": "GMTQTPSPVSAAVGGTVTINCQASQSVYNNYLLSWYQQKPGQPPKRLIYSASTLASGVSSRFKGSGSGTQFTLTISDVQCDDAATYYCLGSYDGNSADCLAFGGGTEVVVKGT", "cdrh1_seq": "GIDPNSDH", "cdrh2_seq": "IYASGTT", "cdrh3_seq": "ATYPNYPTDNL", "cdrl1_seq": "QSVYNNYL", "cdrl2_seq": "SAS", "cdrl3_seq": "LGSYDGNSADCLA", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[93, 103]", "cdrl1_pos": "[24, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 100]", "cdrh3_split": "val", "cdrh3_cluster": "6i9i", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Glycoprotein, Rift valley fever virus", "target_domain": "Domain B", "functional_role": "neutralizing", "evidence_quote": "monoclonal antibody...demonstrate the protective efficacy...neutralizes RVFV"}}}, "tokenized_instruction": [2, 11586, 5655, 1920, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 1920, 2894, 2770, 30, 43, 6020, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11091, 11424, 1927, 12424, 1031, 19469, 9087, 3413, 18, 1920, 11424, 1977, 43, 4346, 4594, 1927, 1920, 19230, 1988, 5823, 1918, 1942, 1920, 4423, 2024, 3148, 16494, 1026, 19, 5330, 17, 2105, 1930, 7383, 5289, 1927, 5726, 1956, 1920, 5058, 22321, 2256, 11914, 16, 2679, 28067, 1920, 7919, 5289, 11109, 1927, 11424, 45, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 3418, 44, 1927, 1920, 9005, 11424, 16, 2154, 1977, 2441, 3743, 17, 3434, 5328, 3772, 1930, 4972, 1925, 6595, 5081, 3560, 3031, 2706, 27965, 18368, 18, 3], "antigen": ["DSFVCFEHKGFDISQCPKIGGHGSKKCTGDAAFCSAYECTAQYANAYCSHA"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A murine Fab (IGHV1/IGKV16-Kappa) targeting the cytochrome c-dependent nitric oxide reductase (cNOR) complex, comprising Nitric oxide reductase subunit B and subunit C from Pseudomonas aeruginosa. Nitric oxide reductase catalyzes the reductive coupling of two nitric oxide molecules at a heme/non-heme Fe center to generate nitrous oxide, functioning as a component of the anaerobic respiratory chain in denitrification. This antibody is designed as a structural tool to facilitate crystallographic determination of the enzyme in reduced and ligand-bound conformational states. What would the HCDRs be?", "target_protein": "EVQLQQSGTVLARPGASVKMSCKASMHWVKQRPGQGLEWIGASYNQKFKGKAKLTAVTSASTAYMELSSLTNEDSAVYYCWGQGTTVTVSSAGYSFTSYWVYPGNSDTSRSSLDGYYVKNWCFDV", "metadata": {"pdb_id": "3wfc", "light_chain_seq": "DIQMTQSPPYLAASPGETITINCRASKSIRKYLAWYQEKPGKTNKLLIYSGSTLQFGIPSRFSGSGSGTEFTLTISSLEPEDFAMYYCQQHNEYPLTFGAGTKLELKRA", "cdrh1_seq": "GYSFTSYW", "cdrh2_seq": "VYPGNSDT", "cdrh3_seq": "SRSSLDGYYVKNWCFDV", "cdrl1_seq": "KSIRKY", "cdrl2_seq": "SGS", "cdrl3_seq": "QQHNEYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3o0r", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV16", "is_engineered": false, "target_antigen": "Nitric oxide reductase subunit B and subunit C, Pseudomonas aeruginosa", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "antibody fragment used to determine structures of reduced and ligand-bound cNOR"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 1016, 17, 12093, 13, 5133, 1920, 9387, 45, 17, 3100, 10233, 7491, 11386, 12, 5940, 1924, 13, 2796, 16, 10351, 10233, 7491, 11386, 5903, 44, 1930, 5903, 45, 2037, 13461, 10830, 18, 10233, 7491, 11386, 17097, 1920, 23335, 7590, 1927, 2288, 10233, 7491, 4206, 2019, 43, 10954, 19, 2447, 17, 10954, 2650, 4102, 1942, 5655, 8686, 1957, 7491, 16, 7295, 1966, 43, 4594, 1927, 1920, 12554, 5481, 4659, 1922, 26319, 3123, 18, 2052, 3533, 1977, 4609, 1966, 43, 4346, 5229, 1942, 6628, 17832, 7063, 1927, 1920, 4113, 1922, 3028, 1930, 5207, 17, 4124, 8523, 4376, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["FASQAVAKPYFVFALILFVGQILFGLIMGLQYVVGDFLFPAIPFNVARMVHTNLLIVWLLFGFMGAAYYLVPEESDCELYSPKLAWILFWVFAAAGVLTILGYLLVPYAGLARLTGNELWPTMGREFLEQPTISKAGIVIVALGFLFNVGMTVLRGRKTAISMVLMTGLIGLALLFLFSFYNPENLTRDKFYWWWVVHLWVEGVWELIMGAILAFVLVKITGVDREVIEKWLYVIIAMALISGIIGTGHHYFWIGVPGYWLWLGSVFSALEPLPFFAMVLFAFNTINRRRRDYPNRAVALWAMGTTVMAFLGAGVWGFMHTLAPVNYYTHGTQLTAAHGHMAFYGAYAMIVMTIISYAMPRLRGIGEAMDNRSQVLEMWGFWLMTVAMVFITLFLSAAGVLQVWLQRMPADGAAMTFMATQDQLAIFYWLREGAGVVFLIGLVAYLLSF", "FTKGMARNIYFGGSVFFILLFLALTYHTEKTLPERTNEAAMSAAVVRGKLVWEQNNCVGCHTLLGEGAYFAPELGNVVGRRGGEEGFNTFLQAWMKIQPLNVPGRRAMPQFHLSEGQVDDLAEFLKWSSKIDTNQWPPNKEG"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A human Fab (IGHV1/IGKV4-Kappa) targeting the Spike protein S1 of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody, binding within the Receptor-binding domain (RBD).", "target_protein": "QVQLVQSGAEVKKPGSSVKVSCKASFSWVRQAPGQGLEWMGGNYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCWGRGTLVTVSSAGGTFNRYAIIPIFGTAARSTRELPEVVDWYFDL", "metadata": {"pdb_id": "8dnn", "light_chain_seq": "DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSAPLTFGGGTKVEIKRT", "cdrh1_seq": "GGTFNRYA", "cdrh2_seq": "IIPIFGTA", "cdrh3_seq": "ARSTRELPEVVDWYFDL", "cdrl1_seq": "QSVLYSSNNKNY", "cdrl2_seq": "WAS", "cdrl3_seq": "QQYYSAPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 102]", "cdrh3_split": "val", "cdrh3_cluster": "8dnn", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Spike protein S1, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibody 80 in complex with SARS-CoV-2 receptor binding domain"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 5133, 1920, 10429, 2213, 4062, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 16, 2743, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 3], "antigen": ["NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A human Fab (IGHV1/IGKV1-Kappa) targeting the Envelope glycoprotein gp160 of Human immunodeficiency virus 1. The Envelope glycoprotein gp160 attaches the virus to the host lymphoid cell by binding to the primary receptor CD4, inducing structural rearrangement that creates a high-affinity binding site for the chemokine co-receptor CCR5. The antibody, 412d, is tyrosine-sulfated and designed to recognize the CCR5 co-receptor binding site on gp120 through sulfotyrosine-mediated interactions. This antibody forms a complex with gp120 and CD4.", "target_protein": "EVQLVQSGAEVKKPGSSVKVSCKASINWVRQAPGQGLEWMGGHYAQRFQGRVSITADESTSTAYMELSSLRSEDTAVFYCWGRGTLVTVSPAGGTFSNYAIIPIFNIAASPYPNDNDAPEEGMSWYFDL", "metadata": {"pdb_id": "2qad", "light_chain_seq": "DIQMTQSPSTLSASVGDRVTITCRASQSISNWLAWYQQKPGRAPKLLMYKASSLKSGVPSRFSGSGSGTEFTLTISSLQSDDFATYYCQQHDSSPYTFGQGTKLEIKRT", "cdrh1_seq": "GGTFSNYA", "cdrh2_seq": "IIPIFNIA", "cdrh3_seq": "ASPYPNDNDAPEEGMSWYFDL", "cdrl1_seq": "QSISNW", "cdrl2_seq": "KAS", "cdrl3_seq": "QQHDSSPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 116]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "2qad", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus 1", "target_domain": "CCR5 co-receptor binding site", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 5133, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 21, 18, 1920, 11262, 11424, 4882, 16954, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1988, 15628, 43, 2149, 17, 5173, 2743, 3200, 1958, 1920, 11673, 2081, 17, 3148, 16238, 18, 1920, 3533, 16, 26039, 1007, 16, 1977, 6941, 17, 26649, 1930, 4609, 1942, 9967, 1920, 16238, 2081, 17, 3148, 2743, 3200, 1990, 16102, 2596, 5141, 26879, 17, 3434, 3719, 18, 2052, 3533, 4952, 43, 2796, 1956, 16102, 1930, 4095, 18, 3], "antigen": ["TENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human Fab, Kick-Off Fab 115 (IGHV3/IGKV3-Kappa), targeting the engineered Ig-like V-type domain of human Tyrosine-protein phosphatase non-receptor type substrate 1 (SIRP\u03b1 Variant 1). SIRP\u03b1 is an immunoglobulin-like cell surface receptor for CD47 that mediates negative regulation of phagocytosis and dendritic cell activation. The antibody is designed to antagonize the CD47/SIRP\u03b1 interaction and potentiate macrophage-mediated antibody-dependent cellular phagocytosis for enhanced anti-cancer immunity.", "target_protein": "DVQLVESGGGVVRPGESLRLSCAASMNWVRQAPGEGLEWVSRDYAESVKGRFTISRDNSENTLYLQMNSLRAEDTAVYYCWGLGALVTVSSAGFSFSSYAINSGGGGTAKQYDWNSFFDY", "metadata": {"pdb_id": "6nmu", "light_chain_seq": "ETVLTQSPATLSVSPGERATLSCRASQTVGSKLAWHQQKPGQAPRLLIYDATNRATGISDRFSGSGSGTDFTLTISSLQTEDSAVYYCQQYYYWPPYRFGGGTKVEIKRT", "cdrh1_seq": "GFSFSSYA", "cdrh2_seq": "INSGGGGT", "cdrh3_seq": "AKQYDWNSFFDY", "cdrl1_seq": "QTVGSK", "cdrl2_seq": "DAT", "cdrl3_seq": "QQYYYWPPYR", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 107]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 97]", "cdrh3_split": "val", "cdrh3_cluster": "6nmu", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Kick-Off Fab 115", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Tyrosine-protein phosphatase non-receptor type substrate 1 (SIRP\u03b1), Homo sapiens", "target_domain": "Ig-like V-type", "functional_role": "other", "evidence_quote": "potently antagonized the CD47/SIRP\u03b1 interaction, potentiated macrophage-mediated antibody-dependent cellular phagocytosis"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 6914, 16, 8191, 12940, 17, 4013, 6914, 10709, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11091, 7021, 17, 3189, 64, 17, 2601, 3418, 1927, 2616, 6941, 17, 2213, 8167, 2447, 17, 3148, 2601, 4510, 21, 12, 4520, 1034, 1071, 6031, 21, 13, 18, 4520, 1034, 1071, 1977, 1925, 11837, 17, 3189, 2024, 3154, 3148, 1958, 29741, 1988, 10412, 3136, 3640, 1927, 13715, 1930, 8104, 2024, 2936, 18, 1920, 3533, 1977, 4609, 1942, 28104, 1920, 29741, 19, 4520, 1034, 1071, 2835, 1930, 23350, 8088, 17, 3434, 3533, 17, 3100, 3689, 13715, 1958, 4256, 2246, 17, 2539, 7611, 18, 3], "antigen": ["ELQVIQPDKSVLVAAGETATLRCTATSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRIGAITPADAGTYYCVKFRKGSPDDVEFKSGAGTELSVRA"]} {"modality_type": "antibody", "text": "Provide the HCDR sequences of an antibody with the following function: A murine Fab, ICSM18 (IGHV1/IGKV4-Kappa), targeting the Major prion protein of Homo sapiens. The Major prion protein plays roles in neuronal development, synaptic plasticity, myelin maintenance, and iron homeostasis, and associates with GPC1 via heparan sulfate chains to target lipid rafts. This antibody forms a complex with the Major prion protein, binding within the Interaction with GRB2, ERI3 and SYN1.", "target_protein": "EVQLQQSGPELVKPGSSVKISCKASLDWVKQSHGKTLEWIGNGYNQKFRGKATLTVDKSSSTAYMELHSLTSEDSAVYYCWGQGTLVTVSSARNTFTDYNVYPNNGVTALYYYDVSY", "metadata": {"pdb_id": "6sv2", "light_chain_seq": "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMHWYQQKSGTSPKRWIYDTSKLASGVPARFSGSGSGTSYSLTISSMEAEDAATYFCHQWRSNPYTFGGGTKLEIKRA", "cdrh1_seq": "RNTFTDYN", "cdrh2_seq": "VYPNNGVT", "cdrh3_seq": "ALYYYDVSY", "cdrl1_seq": "SSVSY", "cdrl2_seq": "DTS", "cdrl3_seq": "HQWRSNPYT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 104]", "cdrl1_pos": "[26, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "2w9e", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "ICSM18", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": false, "target_antigen": "Major prion protein, Homo sapiens", "target_domain": "Interaction with GRB2, ERI3 and SYN1", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3394, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 13772, 8012, 1025, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 16, 5133, 1920, 3044, 16686, 2213, 1927, 16350, 27974, 18, 1920, 3044, 16686, 2213, 5705, 5456, 1922, 5121, 2740, 16, 6251, 8771, 16, 12996, 6291, 16, 1930, 5680, 7622, 16, 1930, 14162, 1956, 27039, 1009, 3454, 22024, 8767, 7835, 1942, 2758, 4486, 21001, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 3044, 16686, 2213, 16, 2743, 2651, 1920, 2835, 1956, 28544, 16, 2668, 1033, 1010, 1930, 2540, 1009, 18, 3], "antigen": ["LGVYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAY"]} {"modality_type": "antibody", "text": "Generate the HCDRs according to this antibody functional description: A murine Fab (IGHV1/IGKV16-Kappa) targeting the cytochrome c-dependent nitric oxide reductase (cNOR) complex, comprising Nitric oxide reductase subunit B and subunit C from Pseudomonas aeruginosa. Nitric oxide reductase catalyzes the reductive coupling of two nitric oxide molecules at a heme/non-heme Fe center to generate nitrous oxide, functioning as a component of the anaerobic respiratory chain in denitrification. This antibody is intended as a structural tool to facilitate crystallographic characterization of the enzyme complex in reduced and ligand-bound states.", "target_protein": "EVQLQQSGTVLARPGASVKMSCKASMHWVKQRPGQGLEWIGASYNQKFKGKAKLTAVTSASTAYMELSSLTNEDSAVYYCWGQGTTVTVSSAGYSFTSYWVYPGNSDTSRSSLDGYYVKNWCFDV", "metadata": {"pdb_id": "3wfe", "light_chain_seq": "DIQMTQSPPYLAASPGETITINCRASKSIRKYLAWYQEKPGKTNKLLIYSGSTLQFGIPSRFSGSGSGTEFTLTISSLEPEDFAMYYCQQHNEYPLTFGAGTKLELKRA", "cdrh1_seq": "GYSFTSYW", "cdrh2_seq": "VYPGNSDT", "cdrh3_seq": "SRSSLDGYYVKNWCFDV", "cdrl1_seq": "KSIRKY", "cdrl2_seq": "SGS", "cdrl3_seq": "QQHNEYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 112]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3o0r", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV16", "is_engineered": false, "target_antigen": "Nitric oxide reductase subunit B and subunit C, Pseudomonas aeruginosa", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "antibody fragment used in structural determination of reduced and ligand-bound cNOR"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 5675, 3147, 1942, 2052, 3533, 3183, 8418, 30, 43, 7135, 6914, 12, 20733, 7390, 19, 7021, 1040, 7390, 1016, 17, 12093, 13, 5133, 1920, 9387, 45, 17, 3100, 10233, 7491, 11386, 12, 5940, 1924, 13, 2796, 16, 10351, 10233, 7491, 11386, 5903, 44, 1930, 5903, 45, 2037, 13461, 10830, 18, 10233, 7491, 11386, 17097, 1920, 23335, 7590, 1927, 2288, 10233, 7491, 4206, 2019, 43, 10954, 19, 2447, 17, 10954, 2650, 4102, 1942, 5655, 8686, 1957, 7491, 16, 7295, 1966, 43, 4594, 1927, 1920, 12554, 5481, 4659, 1922, 26319, 3123, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 6628, 17832, 7285, 1927, 1920, 4113, 2796, 1922, 3028, 1930, 5207, 17, 4124, 4376, 18, 3], "antigen": ["FASQAVAKPYFVFALILFVGQILFGLIMGLQYVVGDFLFPAIPFNVARMVHTNLLIVWLLFGFMGAAYYLVPEESDCELYSPKLAWILFWVFAAAGVLTILGYLLVPYAGLARLTGNELWPTMGREFLEQPTISKAGIVIVALGFLFNVGMTVLRGRKTAISMVLMTGLIGLALLFLFSFYNPENLTRDKFYWWWVVHLWVEGVWELIMGAILAFVLVKITGVDREVIEKWLYVIIAMALISGIIGTGHHYFWIGVPGYWLWLGSVFSALEPLPFFAMVLFAFNTINRRRRDYPNRAVALWAMGTTVMAFLGAGVWGFMHTLAPVNYYTHGTQLTAAHGHMAFYGAYAMIVMTIISYAMPRLRGIGEAMDNRSQVLEMWGFWLMTVAMVFITLFLSAAGVLQVWLQRMPADGAAMTFMATQDQLAIFYWLREGAGVVFLIGLVAYLLSF", "FTKGMARNIYFGGSVFFILLFLALTYHTEKTLPERTNEAAMSAAVVRGKLVWEQNNCVGCHTLLGEGAYFAPELGNVVGRRGGEEGFNTFLQAWMKIQPLNVPGRRAMPQFHLSEGQVDDLAEFLKWSSKIDTNQWPPNKEG"]} {"modality_type": "antibody", "text": "Generate the heavy chain CDRs for an antibody that will have the following function: A human Fab (IGHV4/IGLV2-Lambda) targeting the clade A/E 93TH057 HIV-1 gp120 core of Human immunodeficiency virus 1. The antibody is designed to engage the CD4-induced (CD4i) epitope and confer protection via antibody-dependent cellular cytotoxicity (ADCC) mechanisms. This antibody forms a complex with gp120 in its CD4-bound conformation state.", "target_protein": "EVQLVESGPGLVKPSQTLSLTCTVSWSWIRQHPGKGLEWIGNYYNPSLKSRLTISVDTTQNQFSLKLTSVTAADTAVYYCWGQGTLVTVSSAGASISSGGYFIYYIGNTARVPRLRGGNYFDS", "metadata": {"pdb_id": "5kjr", "light_chain_seq": "QSVLTQPASVSGSPGQSITISCTGTSSDVGGYKYVSWYQQHPDKAPKLMIYEVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTWVFGGGTKLTVLGQ", "cdrh1_seq": "GASISSGGYF", "cdrh2_seq": "IYYIGNT", "cdrh3_seq": "ARVPRLRGGNYFDS", "cdrl1_seq": "SSDVGGYKY", "cdrl2_seq": "EVS", "cdrl3_seq": "SSYTSSSTWV", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 110]", "cdrl1_pos": "[25, 33]", "cdrl2_pos": "[51, 53]", "cdrl3_pos": "[90, 99]", "cdrh3_split": "val", "cdrh3_cluster": "5kjr", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "clade A/E 93TH057 HIV-1 gp120 core, Human immunodeficiency virus 1", "target_domain": null, "functional_role": "other", "evidence_quote": "CD4-induced antibodies capable of potent antibody-dependent cellular cytotoxicity"}}}, "tokenized_instruction": [2, 5655, 1920, 7881, 4659, 20170, 1036, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1006, 19, 28961, 15755, 17, 18279, 13, 5133, 1920, 11315, 43, 19, 47, 6156, 1963, 15264, 1027, 3525, 17, 21, 16102, 4728, 1927, 2616, 13141, 3413, 21, 18, 1920, 3533, 1977, 4609, 1942, 11580, 1920, 4095, 17, 2719, 12, 4095, 1033, 13, 10095, 1930, 7909, 6202, 3454, 3533, 17, 3100, 3689, 8470, 12, 25899, 13, 3531, 18, 2052, 3533, 4952, 43, 2796, 1956, 16102, 1922, 2496, 4095, 17, 4124, 7748, 3360, 18, 3], "antigen": ["VWKDADTTLFCASDAKAHETEVHNVAATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQWLQPCVKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCIKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A human Fab (IGHV1/IGKV3-Kappa), one of three antibodies in a complex (CB6 mutant, S309, and S304), targeting the engineered Spike protein S1 of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors including ACE2, TFRC, GRM2, NRP1/NRP2, integrin, and ASGR1, and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding and protease cleavage. This antibody forms a complex with the Spike protein S1 within the Receptor-binding domain (RBD).", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVTVSSAGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "8wpy", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRT", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Spike protein S1, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 2340, 1927, 2559, 3788, 1922, 43, 2796, 12, 5529, 1016, 3606, 16, 6080, 13192, 16, 1930, 6080, 14743, 13, 16, 5133, 1920, 11091, 10429, 2213, 4062, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 2710, 8298, 1028, 16, 26817, 1030, 16, 2398, 8224, 16, 5214, 5113, 19, 5214, 5991, 16, 8920, 16, 1930, 1966, 2299, 1009, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 1930, 7154, 6404, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 10429, 2213, 4062, 2651, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 18, 3], "antigen": ["TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab, 4E10 (IGHV1/IGKV3-Kappa), targeting the Envelope glycoprotein gp160 of Human immunodeficiency virus type 1. The Envelope glycoprotein gp160 attaches the virus to the host lymphoid cell by binding to the primary receptor CD4, inducing structural rearrangement and enabling viral entry. The antibody is designed as a broadly neutralizing antibody targeting the MPER region, which requires penetration into the viral membrane interface and specific interactions with the transmembrane domain to achieve neutralization. Please output the HCDRs.", "target_protein": "QVQLVQSGAEVKRPGSSVTVSCKASLSWVRQAPGRGLEWMGGNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCWGQGTLVTVSSAGGSFSTYAVIPLLTITAREGTTPGKPIGAFAH", "metadata": {"pdb_id": "5x08", "light_chain_seq": "EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRT", "cdrh1_seq": "GGSFSTYA", "cdrh2_seq": "VIPLLTIT", "cdrh3_seq": "AREGTTPGKPIGAFAH", "cdrl1_seq": "QSVGNNK", "cdrl2_seq": "GAS", "cdrl3_seq": "QQYGQSLST", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 111]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 97]", "cdrh3_split": "val", "cdrh3_cluster": "5x08", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "4E10", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Envelope glycoprotein gp160, Human immunodeficiency virus type 1", "target_domain": "MPER; binding to GalCer", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing anti-HIV-1 antibody 4E10"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 10800, 2930, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 4882, 16954, 1927, 2616, 13141, 3413, 2601, 21, 18, 1920, 11262, 11424, 4882, 16954, 5823, 1918, 1920, 3413, 1942, 1920, 4423, 11751, 2024, 2007, 2743, 1942, 1920, 3065, 3148, 4095, 16, 7834, 4346, 14154, 1930, 12180, 4324, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 5438, 1915, 3031, 16, 2154, 5474, 12006, 2460, 1920, 4324, 3260, 6854, 1930, 2487, 3719, 1956, 1920, 9117, 3418, 1942, 6230, 14377, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["NWFDITNWLWYIKK"]} {"modality_type": "antibody", "text": "A human Fab, IMC-11F8 (IGHV4/IGKV3-Kappa), targeting an engineered isolated domain III of the Epidermal growth factor receptor. The Epidermal growth factor receptor is a receptor tyrosine kinase that binds ligands of the EGF family and activates multiple downstream signaling cascades to convert extracellular cues into cellular responses. The antibody is designed to inhibit EGFR signaling as a therapeutic anticancer strategy. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "QVQLQESGPGLVKPSQTLSLTCTVSWSWIRQPPGKGLEWIGYDYNPSLKSRVTMSVDTSKNQFSLKVNSVTAADTAVYYCWGQGTLVTVSSAGGSISSGDYYIYYSGSTARVSIFGVGTFDY", "metadata": {"pdb_id": "3b2u", "light_chain_seq": "EIVMTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCHQYGSTPLTFGGGTKAEIKRT", "cdrh1_seq": "GGSISSGDYY", "cdrh2_seq": "IYYSGST", "cdrh3_seq": "ARVSIFGVGTFDY", "cdrl1_seq": "QSVSSY", "cdrl2_seq": "DAS", "cdrl3_seq": "HQYGSTPLT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "3b2u", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "IMC-11F8", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Epidermal growth factor receptor, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "EGFR inhibition by an antibody drug IMC-11F8"}}}, "tokenized_instruction": [2, 43, 2616, 6914, 16, 2042, 1030, 17, 2513, 1038, 1025, 12, 20733, 1020, 1006, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1925, 11091, 3937, 3418, 4337, 1927, 1920, 9844, 2905, 2991, 3148, 18, 1920, 9844, 2905, 2991, 3148, 1977, 43, 3148, 6941, 4016, 1988, 6876, 6908, 1927, 1920, 4451, 3416, 1930, 9094, 3137, 5863, 3197, 15967, 1942, 14450, 5329, 8972, 2460, 3689, 3387, 18, 1920, 3533, 1977, 4609, 1942, 2875, 5775, 3197, 1966, 43, 4272, 11515, 4884, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["EKKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSC"]} {"modality_type": "antibody", "text": "A human Fab, P5A-3C12 (IGHV2/IGKV4-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor, initiating infection, and mediates fusion of viral and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that disrupts the interaction between the receptor-binding domain (RBD) and ACE2, binding within the RBD. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "TLKESGPTLVKPTQTLTLTCTFSVGWIRQPPGKALEWLALRYSPSLKSRLTITKDTSKNQVVLTMTNMDPVDTATYYCWGQGTLVTVSSGFSLSTSGVGIYWDDDKAHSLFLTVGYSSSWSPFDY", "metadata": {"pdb_id": "7d0b", "light_chain_seq": "DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTPHTFGQGTKLEIK", "cdrh1_seq": "GFSLSTSGVG", "cdrh2_seq": "IYWDDDK", "cdrh3_seq": "AHSLFLTVGYSSSWSPFDY", "cdrl1_seq": "QSVLYSSNNKNY", "cdrl2_seq": "WAS", "cdrl3_seq": "QQYYSTPHT", "cdrh1_pos": "[23, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 113]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 102]", "cdrh3_split": "val", "cdrh3_cluster": "7d0b", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "P5A-3C12", "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGKV4", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibodies capable of disrupting proper interaction between the receptor binding domain (RBD) and ACE2"}}}, "tokenized_instruction": [2, 43, 2616, 6914, 16, 18974, 1019, 17, 7550, 3112, 12, 20733, 15755, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 18605, 1920, 2835, 2192, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 1930, 8298, 1028, 16, 2743, 2651, 1920, 25780, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVMESEFRVYSSANNCTFEYVSKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD"]} {"modality_type": "antibody", "text": "What would the HCDRs of an antibody with the following function look like? Here is the function: A human Fab, P5A-3C12 (IGHV2/IGKV4-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptor ACE2, initiating infection, and mediates fusion of the virion and cellular membranes by functioning as a class I viral fusion protein. The antibody is designed as a neutralizing antibody that disrupts the interaction between the receptor-binding domain (RBD) and ACE2, binding within the RBD.", "target_protein": "TLKESGPTLVKPTQTLTLTCTFSVGWIRQPPGKALEWLALRYSPSLKSRLTITKDTSKNQVVLTMTNMDPVDTATYYCWGQGTLVTVSSGFSLSTSGVGIYWDDDKAHSLFLTVGYSSSWSPFDY", "metadata": {"pdb_id": "7d0d", "light_chain_seq": "DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTPHTFGQGTKLEIK", "cdrh1_seq": "GFSLSTSGVG", "cdrh2_seq": "IYWDDDK", "cdrh3_seq": "AHSLFLTVGYSSSWSPFDY", "cdrl1_seq": "QSVLYSSNNKNY", "cdrl2_seq": "WAS", "cdrl3_seq": "QQYYSTPHT", "cdrh1_pos": "[23, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 113]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 102]", "cdrh3_split": "val", "cdrh3_cluster": "7d0b", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "P5A-3C12", "antibody_format": "Fab", "heavy_subclass": "IGHV2", "light_subclass": "IGKV4", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "Receptor-binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "neutralizing antibodies capable of disrupting proper interaction between the receptor binding domain (RBD) of the viral spike (S) protein and the receptor angiotensin converting enzyme 2 (ACE2)"}}}, "tokenized_instruction": [2, 4663, 2962, 1920, 27203, 5675, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 43, 2616, 6914, 16, 18974, 1019, 17, 7550, 3112, 12, 20733, 15755, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 3148, 8298, 1028, 16, 12410, 2909, 16, 1930, 10412, 5289, 1927, 1920, 19230, 1930, 3689, 5726, 2007, 7295, 1966, 43, 2921, 51, 4324, 5289, 2213, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 18605, 1920, 2835, 2192, 1920, 3148, 17, 2743, 3418, 12, 25780, 13, 1930, 8298, 1028, 16, 2743, 2651, 1920, 25780, 18, 3], "antigen": ["AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVMESEFRVYSSANNCTFEYVSKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab, DH1047 (IGHV1/IGKV4-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors ACE2 and CLEC4M/DC-SIGNR, initiating infection and inducing conformational changes that expose the fusion peptide. The antibody is designed as a broadly neutralizing antibody targeting a conserved epitope within the Receptor binding domain (RBD) that confers protection against SARS-CoV, bat coronaviruses, and multiple SARS-CoV-2 variants.", "target_protein": "QVQLVQSGAEVKKPGASVQVSCQASIHWVRQAPGQGLEWMGIIYAQGFQGRVTMTRDTSLNTIYLELSSLRSEDTAVYYCWGQGTLVTVSSAANTFTNHYIYPTGGNTARDVRVDDSWSGYDLLSGGTYFDY", "metadata": {"pdb_id": "7sg4", "light_chain_seq": "DIVMTQSPDSLAVSLGERATINCRSSQSVLYSSNNENYLAWYQQKPGQPPKLLIYWASTRESGIPDRFSGSGSGTDFTLTISRLQAEDVAVYYCQQYYSLPRTFGQGTKVEIKRT", "cdrh1_seq": "ANTFTNHY", "cdrh2_seq": "IYPTGGNT", "cdrh3_seq": "ARDVRVDDSWSGYDLLSGGTYFDY", "cdrl1_seq": "QSVLYSSNNENY", "cdrl2_seq": "WAS", "cdrl3_seq": "QQYYSLPRT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 119]", "cdrl1_pos": "[26, 37]", "cdrl2_pos": "[55, 57]", "cdrl3_pos": "[94, 102]", "cdrh3_split": "val", "cdrh3_cluster": "8dtk", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DH1047", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV4", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus", "target_domain": "Receptor binding domain (RBD)", "functional_role": "neutralizing", "evidence_quote": "neutralization of SARS-CoV and SARS-CoV-2 variants; broadly protective antibody"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6781, 15231, 1027, 12, 20733, 7390, 19, 7021, 1040, 1020, 1006, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 8298, 1028, 1930, 2965, 17875, 1035, 19, 5330, 17, 2105, 1005, 16, 12410, 2909, 1930, 7834, 8523, 2840, 1988, 21369, 1920, 5289, 4207, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 43, 5305, 10095, 2651, 1920, 3148, 2743, 3418, 12, 25780, 13, 1988, 16556, 6202, 3316, 20466, 17, 6083, 16, 11579, 5548, 26979, 16, 1930, 3137, 20466, 17, 6083, 17, 22, 4936, 18, 3], "antigen": ["SSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYFVGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDPKTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLLRSTSQKSIVAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAAEQDRNTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIEDLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDNTFVSGNCDVVIGIINNTVYDPLQPELDS"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab, Z2B3 D102R (IGHV1/IGLV2-Lambda), targeting the Neuraminidase of Influenza A virus. Neuraminidase catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates to facilitate virus release and spread, and plays a role in viral budding, host range restriction, and virulence. The antibody is designed as a neutralizing antibody that inhibits neuraminidase enzymatic activity and protects against influenza infection, binding within the Head of neuraminidase at the conserved active site. Please output the HCDRs.", "target_protein": "EVQLVQSGAEVKKPGSSVKVSCKASFSWVRQAPGQGLEWMGGNYAQKFQGRVTITADESTSTAYMELSSLKSEDTAVYYCWGQGTTVTVSSAGGPFSSYGIIPVYGTTARDLQRTPMVDRIIGSYYYYNGLDV", "metadata": {"pdb_id": "6lxk", "light_chain_seq": "SVLTQPASVSGSPGQSITISCTGASSDVGDYNYVSWYQQHPGKAPKLMIYDVSNRPSGVSNRFSGSKSGDTASLTISGLQAEDEADYYCSSYTRSSSVVFGGGTKLTVLGQ", "cdrh1_seq": "GGPFSSYG", "cdrh2_seq": "IIPVYGTT", "cdrh3_seq": "ARDLQRTPMVDRIIGSYYYYNGLDV", "cdrl1_seq": "SSDVGDYNY", "cdrl2_seq": "DVS", "cdrl3_seq": "SSYTRSSSVV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 120]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "6lxj", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "Z2B3 D102R", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "Neuraminidase, Influenza A virus", "target_domain": "Head of neuraminidase", "functional_role": "neutralizing", "evidence_quote": "Z2B3-D102R can protect mice from A/Serbia/NS-601/2014 H1N1 virus infection"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 68, 9385, 1010, 8524, 11636, 1005, 12, 20733, 7390, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 29831, 1927, 7108, 43, 3413, 18, 29831, 17097, 1920, 6025, 1927, 4262, 20436, 2687, 4248, 2037, 4324, 1930, 3689, 4235, 30378, 2209, 1942, 6628, 3413, 4012, 1930, 6441, 16, 1930, 5705, 43, 2770, 1922, 4324, 15909, 16, 4423, 3109, 7587, 16, 1930, 9304, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7042, 29831, 8145, 2455, 1930, 14576, 3316, 7108, 2909, 16, 2743, 2651, 1920, 4469, 1927, 29831, 2019, 1920, 5305, 3500, 3200, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["VKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDSGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTIMTDGPSDGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGVFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRKGFEMIWDPNGWTGTDNKFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPEENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTIDK"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A muskrat Fab, YN9048 (IGHV1/IGKV10-Kappa), targeting the engineered myristoylated PreS1 protein fragment of Hepatitis B virus. The PreS1 domain of the large envelope protein binds to the host receptor sodium-taurocholate cotransporting polypeptide (NTCP) to initiate viral entry. This antibody forms a complex with the PreS1 protein within the Pre-S domain.", "target_protein": "EVQLQESGPELVKPGDSVKMSCKASMDWVKQNHGKSLEWIGYNYNQKFKGKATLTVDKSSSTAYMELHSLTSEDSAVYYCWGQGTLVTVSAAGYTFTDYYIYPYNGGTARRGRFPWLAY", "metadata": {"pdb_id": "8hrx", "light_chain_seq": "DIVMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVRVLIYYTSRLHSGVPSRFSGSGSGTDFSLTISNLEPEDIATYYCQQYSKFPWTFGGGTKLEIKRA", "cdrh1_seq": "GYTFTDYY", "cdrh2_seq": "IYPYNGGT", "cdrh3_seq": "ARRGRFPWLAY", "cdrl1_seq": "QDISNY", "cdrl2_seq": "YTS", "cdrl3_seq": "QQYSKFPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8hrx", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "YN9048", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV10", "is_engineered": true, "target_antigen": "PreS1 protein (Fragment), Hepatitis B virus", "target_domain": "Pre-S", "functional_role": "unknown", "evidence_quote": null}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 3177, 21783, 1926, 6914, 16, 67, 28955, 14743, 1025, 12, 20733, 7390, 19, 7021, 1040, 7390, 1008, 17, 12093, 13, 16, 5133, 1920, 11091, 20234, 10921, 1981, 2244, 1009, 2213, 5302, 1927, 7977, 44, 3413, 18, 1920, 2244, 1009, 3418, 1927, 1920, 3103, 11262, 2213, 6876, 1942, 1920, 4423, 3148, 5227, 17, 7462, 24182, 8649, 14817, 29776, 13022, 12, 5891, 10020, 13, 1942, 11051, 4324, 6904, 18, 2052, 3533, 4952, 43, 2796, 1956, 1920, 2244, 1009, 2213, 2651, 1920, 2097, 17, 61, 3418, 18, 3], "antigen": ["GTNLSVPNPLGFFPDHQLDPAFKANSENPDWDLNPHKDNWPDANKVG", "NFTLPPNFGKRPTDLALSVILVFMLFFIMLSLGCTMEFSKIKAHLWKPKGLAIALVAQYGIMPLTAFVLGKVFRLKNIEALAILVCGCSPGGNLSNVFSLAMKGDMNLSIVMTTCSTFCALGMMPLLLYIYSRGIYDGDLKDKVPYKGIVISLVLVLIPCTIGIVLKSKRPQYMRYVIKGGMIIILLCSVAVTVLSAINVGKSIMFAMTPLLIATSSLMPFIGFLLGYVLSALFCLNGRCRRTVSMETGCQNVQLCSTILNVAFPPEVIGPLFFFPLLYMIFQLGEGLLLIAIFWCYEKFKT"]} {"modality_type": "antibody", "text": "I want to build an antibody that will have the following function: A murine Fab, N1D10 (IGHV5/IGKV1-Kappa), targeting the engineered Envelopment polyprotein of Severe fever with thrombocytopenia syndrome virus. The Envelopment polyprotein is a structural component of the virion that shields the hydrophobic fusion loops of glycoprotein C and interacts with glycoprotein N, acting as a class II fusion protein activated upon acidification. N1D10 is a cross-reactive antibody recognizing Gn proteins across SFTSV, HRTV, and GTV, and forms a complex with the Envelopment polyprotein. Generate the corresponding HCDRs.", "target_protein": "EVKLVESGGGLVQPGGSLKLSCAASMSWVRQTPEKRLEWVAYYYPDTVKGRFTISRDNAKNTLYLQMSSLNSEDTAMYYCWGAGTTVTVSSAGFTFSTYTISNGGGSTARSYGNFDV", "metadata": {"pdb_id": "8xk8", "light_chain_seq": "DVVMTQTPLSLPVSFGDQVSISCRSSQSLANSYGNTYLSWYLHKPGQSPQLLIYGISKRFSGVPDRFSGSGSGTDFTLKISTIKPEDLGMYYCLQGTHQPWTFGGGTKLEIKRT", "cdrh1_seq": "GFTFSTYT", "cdrh2_seq": "ISNGGGST", "cdrh3_seq": "ARSYGNFDV", "cdrl1_seq": "QSLANSYGNTY", "cdrl2_seq": "GIS", "cdrl3_seq": "LQGTHQPWT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 104]", "cdrl1_pos": "[26, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "8xk8", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "N1D10", "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Envelopment polyprotein, Severe fever with thrombocytopenia syndrome virus", "target_domain": null, "functional_role": "other", "evidence_quote": "cross-reactive mAbs (S1E9 and N1D10), which recognize the Gn proteins of SFTSV, HRTV, and GTV"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 10071, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 7135, 6914, 16, 13007, 7240, 1008, 12, 20733, 1020, 1015, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 9840, 2017, 6240, 5684, 1927, 4010, 9087, 1956, 17100, 4741, 3413, 18, 1920, 9840, 2017, 6240, 5684, 1977, 43, 4346, 4594, 1927, 1920, 19230, 1988, 19397, 1036, 1920, 7919, 5289, 11109, 1927, 11424, 45, 1930, 9034, 1956, 11424, 56, 16, 8290, 1966, 43, 2921, 2890, 5289, 2213, 4128, 4073, 19641, 18, 13007, 7240, 1008, 1977, 43, 3567, 17, 6079, 3533, 15667, 9005, 2697, 3436, 6347, 1973, 1020, 16, 20159, 1020, 16, 1930, 4637, 1020, 16, 1930, 4952, 43, 2796, 1956, 1920, 9840, 2017, 6240, 5684, 18, 5655, 1920, 3980, 27203, 5675, 18, 3], "antigen": ["TGPIICAGPIHSNKSADIPHLLGYSEKICQIDRLIHVSSWLRNHSQFQGYVGQRGGRSQVSYYPAENSYSRWSGLLSPCDADWLGMLVVKKAKGSDMIVPGPSYKGKVFFERPTFDGYVGWGCGSGKSRTESGELCSSDSRTSSGLLPSDRVLWIGDVACQPMTPIPEETFLELKSFSQSEFPDICKIDGIVFNQCEGESLPQPFDVAWMDVGHSHKIIMREHKTKWVQESSSKDFVCYKEGTGPCSESEEKTCKTSGSCRGDMQFCKVAGCEAKCRCSLVHKPGEVVVSYGGMRVRPKCYGFSRMMATLEVS"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human single-chain Fv (scFv), R11 (IGHV1/IGKV1-Kappa), targeting the Kringle domain of the Inactive tyrosine-protein kinase transmembrane receptor ROR1 expressed on tumor cells. ROR1 is a receptor for ligand WNT5A that activates downstream NFkB signaling and via IGFBP5 forms a complex with ERBB2 to enhance CREB oncogenic signaling. The antibody is designed as a T cell-engaging bispecific antibody that recruits cytolytic T cells to ROR1-expressing tumor cells through a membrane-proximal epitope conserved between human and mouse ROR1.", "target_protein": "VKESEGDLVTPAGNLTLTCTASISWVRQAPGKGLEWIGFWYASWVKGRFTISRTSTTVDLKMTSLTTDDTATYFCWGPGTLVTISGSDINDYPINSGGSTARGYSTYYGDFNI", "metadata": {"pdb_id": "6ban", "light_chain_seq": "ELVMTQTPSSTSGAVGGTVTINCQASQSIDSNLAWFQQKPGQPPTLLIYRASNLASGVPSRFSGSRSGTEYTLTISGVQREDAATYYCLGGVGNVSYRTSFGGGTEVVVK", "cdrh1_seq": "GSDINDYP", "cdrh2_seq": "INSGGST", "cdrh3_seq": "ARGYSTYYGDFNI", "cdrl1_seq": "QSIDSN", "cdrl2_seq": "RAS", "cdrl3_seq": "LGGVGNVSYRTS", "cdrh1_pos": "[22, 29]", "cdrh2_pos": "[47, 53]", "cdrh3_pos": "[90, 102]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 99]", "cdrh3_split": "val", "cdrh3_cluster": "6ban", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "R11", "antibody_format": "scFv", "heavy_subclass": "IGHV1", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Inactive tyrosine-protein kinase transmembrane receptor ROR1, Homo sapiens", "target_domain": "Kringle", "functional_role": "other", "evidence_quote": "T cell-engaging bispecific antibody targeting ROR1 for retargeting cytolytic T cells toward tumor cells"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 2957, 17, 4659, 11417, 12, 19863, 13, 16, 12041, 1009, 12, 20733, 7390, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 6203, 1941, 1952, 3418, 1927, 1920, 9078, 6941, 17, 2213, 4016, 9117, 3148, 17399, 1009, 3198, 1990, 2798, 2094, 18, 17399, 1009, 1977, 43, 3148, 1958, 5207, 26630, 1988, 9094, 5863, 4651, 11228, 3197, 1930, 3454, 16568, 1015, 4952, 43, 2796, 1956, 17291, 1942, 4826, 13268, 11446, 3197, 18, 1920, 3533, 1977, 4609, 1966, 43, 62, 2024, 17, 15888, 7266, 10231, 3533, 1988, 18855, 29198, 62, 2094, 1942, 17399, 1009, 17, 4590, 2798, 2094, 2596, 43, 3260, 17, 6863, 10095, 5305, 2192, 2616, 1930, 3321, 17399, 1009, 18, 3], "antigen": ["HKCYNSTGVDYRGTVSVTKSGRQCQPWNSQYPHTHTFTALRFPELNGGHSYCRNPGNQKEAPWCFTLDENFKSDLCDIPAC"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A murine Fab (IGHV5/IGKV6-Kappa) targeting the engineered Oxalate:formate antiporter of Oxalobacter formigenes. The Oxalate:formate antiporter catalyzes the exchange of divalent oxalate with monovalent formate at the plasma membrane, driving a proton-motive metabolic cycle that enables ATP synthesis. This antibody is intended as a structural tool to stabilize and visualize the ligand-free outward-facing conformation of the transporter.", "target_protein": "EVMLVESGGGLVKPGGSLKLSCAASMSWVRQTPEKRLEWVALYYPDSVKGRFTISRDKARNILHLQMSSLRSEDTAMYFCWGQGTLVTVSAAGFTFSNYAISSGGYTARGPYDFDDGPPFGN", "metadata": {"pdb_id": "8hpj", "light_chain_seq": "DIVLTQSQKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALIYSASYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQYNSYPLTFGAGTKLELKT", "cdrh1_seq": "GFTFSNYA", "cdrh2_seq": "ISSGGYT", "cdrh3_seq": "ARGPYDFDDGPPFGN", "cdrl1_seq": "QNVGTN", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYNSYPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "8hpj", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV5", "light_subclass": "IGKV6", "is_engineered": true, "target_antigen": "Oxalate:formate antiporter, Oxalobacter formigenes", "target_domain": null, "functional_role": "structural_tool", "evidence_quote": "Crystal structure of the bacterial oxalate transporter OxlT in a ligand-free outward-facing form"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 7135, 6914, 12, 20733, 1020, 1015, 19, 7021, 1040, 25606, 17, 12093, 13, 5133, 1920, 11091, 25069, 30, 25741, 2246, 24095, 1927, 18512, 5883, 2386, 21475, 18, 1920, 25069, 30, 25741, 2246, 24095, 17097, 1920, 6818, 1927, 21610, 25069, 1956, 28685, 25741, 2019, 1920, 3582, 3260, 16, 9228, 43, 8433, 17, 7038, 1021, 4487, 4048, 1988, 10217, 4498, 4271, 18, 2052, 3533, 1977, 11214, 1966, 43, 4346, 5229, 1942, 13448, 1930, 13159, 1920, 5207, 17, 3294, 18411, 17, 15424, 7748, 1927, 1920, 9054, 18, 3], "antigen": ["GLLGNRWFYLVLAVLLMCMISGVQYSWTLYANPVKDNLGVSLAAVQTAFTLSQVIQAGSQPGGGYFVDKFGPRIPLMFGGAMVLAGWTFMGMVDSVPALYALYTLAGAGVGIVYGIAMNTANRWFPDKRGLASGFTAAGYGLGVLPFLPLISSVLKVEGVGAAFMYTGLIMGILIILIAFVIRFPGIVVTDKDFNSGEMLRTPQFWVLWTAFFSVNFGGLLLVANSVPYGRSLGLAAGVLTIGVSIQNLFNGGCRPFWGFVSDKIGRYKTMSVVFGINAVVLALFPTIAALGDVAFIAMLAIAFFTWGGSYALFPSTNSDIFGTAYSARNYGFFWAAKATASIFGGGLGAAIATNFGWNTAFLITAITSFIAFALATFVIPRMGRPVKKMVKL"]} {"modality_type": "antibody", "text": "Can you generate an antibody's HCDRs given the following functional description? A human Fab, DH511.1 (IGHV3/IGKV1-Kappa), targeting the membrane-proximal external region (MPER) peptide of HIV-1 gp41. The gp41 MPER is part of the envelope glycoprotein that mediates fusion of viral and host cell membranes during entry. The antibody is designed as a broadly neutralizing antibody targeting the distal MPER epitope, recognizing a transiently exposed intermediate conformation of gp41 that is induced after CD4-mediated Env activation, binding within the Retroviral envelope protein GP41-like domain.", "target_protein": "EVQLVESGGGLVKPGGSLRLSCAASMSWVRQAPGKGLEWVGREYAAPVRGRFTISRDDSRDTLYLQMTSLKIEDSGRYFCWGKGTTVTVSSAGFTFSNTWISRNKDGAKTTADLGEPVVSRFFEWGSYYYYMDL", "metadata": {"pdb_id": "5u3j", "light_chain_seq": "DIQMTQSPSPLSASVGDTVTITCRASQKISDYLNWYQQKPGRAPKILIYAASKLGSGVPSRFSGSGYGRDFTLTITGLQPEDFATYYCQEAYSSTPTLTFGQGTRLDLKRT", "cdrh1_seq": "GFTFSNTW", "cdrh2_seq": "ISRNKDGAKT", "cdrh3_seq": "TADLGEPVVSRFFEWGSYYYYMDL", "cdrl1_seq": "QKISDY", "cdrl2_seq": "AAS", "cdrl3_seq": "QEAYSSTPTLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 59]", "cdrh3_pos": "[98, 121]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 98]", "cdrh3_split": "val", "cdrh3_cluster": "5u3m", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DH511.1", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "gp41 MPER peptide, Human immunodeficiency virus 1", "target_domain": "Retroviral envelope protein GP41-like", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing distal MPER bnAbs"}}}, "tokenized_instruction": [2, 2112, 6253, 5655, 1925, 3533, 11, 61, 27203, 5675, 3258, 1920, 2894, 3183, 8418, 35, 43, 2616, 6914, 16, 6781, 7912, 1009, 18, 21, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 3260, 17, 6863, 5771, 3031, 12, 5438, 1915, 13, 4207, 1927, 3525, 17, 21, 25618, 18, 1920, 25618, 5438, 1915, 1977, 3131, 1927, 1920, 11262, 11424, 1988, 10412, 5289, 1927, 4324, 1930, 4423, 2024, 5726, 2409, 6904, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 3533, 5133, 1920, 6583, 5438, 1915, 10095, 16, 15667, 43, 12145, 4616, 6129, 7748, 1927, 25618, 1988, 1977, 2719, 2256, 4095, 17, 3434, 11118, 2936, 16, 2743, 2651, 1920, 16599, 11262, 2213, 25618, 17, 3189, 3418, 18, 3], "antigen": ["NEQELLELDKWASLWNWFDITNWLWYIRR"]} {"modality_type": "antibody", "text": "I want to make an antibody that can have this function: A human Fab, G9E (IGHV3/IGLV2-Lambda), targeting the engineered Envelope protein E of Zika virus. The Envelope protein E is a surface protein required for viral entry into host cells. The antibody is designed as a neutralizing antibody that cross-links E protein homodimers to prevent the low pH-triggered conformational changes necessary for viral membrane fusion and genome release into the host cytoplasm. Can you generate its HCDRs?", "target_protein": "RVHLVESGGGVVQPGRSLRLSCVASMHWVRQAPGKGLEWVAIYYADSVKGRFTISRDNSKNTLFLQMNRLRAEDTALYYCWGQGTLVTVSSAGFAFSNYHIWDDGSDQVGGSSAYNGDNGWREAASLDD", "metadata": {"pdb_id": "8dv6", "light_chain_seq": "SALTQPASVSGSPGQSITIFCSGSSNDVGGYNYVSWYQQYPGKVPKLLIYDVNSRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSRRTWVFGGGTIVTVLGQ", "cdrh1_seq": "GFAFSNYH", "cdrh2_seq": "IWDDGSDQ", "cdrh3_seq": "VGGSSAYNGDNGWREAASLDD", "cdrl1_seq": "SNDVGGYNY", "cdrl2_seq": "DVN", "cdrl3_seq": "SSYTSRRTWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 116]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "7yar", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "G9E", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV2", "is_engineered": true, "target_antigen": "Envelope protein E, Zika virus ZIKV/Human/Cambodia/FSS13025/2010", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "antibody blocks infection by cross-linking and paralyzing proteins on the viral surface required for the virus to enter cells"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 5144, 1925, 3533, 1988, 2112, 2162, 2052, 2347, 30, 43, 2616, 6914, 16, 25129, 1021, 12, 20733, 1020, 1010, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 11091, 11262, 2213, 47, 1927, 28593, 3413, 18, 1920, 11262, 2213, 47, 1977, 43, 3154, 2213, 3414, 1958, 4324, 6904, 2460, 4423, 2094, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 3567, 17, 10069, 47, 2213, 29227, 1942, 4625, 1920, 2330, 2087, 17, 9436, 8523, 2840, 4680, 1958, 4324, 3260, 5289, 1930, 3843, 4012, 2460, 1920, 4423, 5239, 18, 2112, 6253, 5655, 2496, 27203, 5675, 35, 3], "antigen": ["IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGS"]} {"modality_type": "antibody", "text": "Design the HCDRs for an antibody that will have the following function: A human Fab, 3P10 (IGHV9/IGKV3-Kappa), targeting an engineered GDNF family receptor alpha-like (GFRAL) of Homo sapiens. GFRAL is a brainstem-restricted receptor for the GDF15 hormone that triggers an aversive response and mediates GDF15-induced autophosphorylation and activation of the RET tyrosine kinase receptor, leading to activation of MAPK and AKT signaling pathways and expression of genes involved in lipid metabolism. The antibody is designed to antagonize the GDF15-GFRAL-RET signaling axis by preventing GDF15-driven interaction of RET with GFRAL, thereby reversing cancer cachexia.", "target_protein": "IQLVQSGPELKKPGETVKISCKASVIWVKQAPGKALKWMGWTYADDLKGRFAFSLETSASSASLQINNLKNEDTATYFCWGQGTTLTVSSAGYTFTDYGINTYTGEPARRYGPEDIDY", "metadata": {"pdb_id": "6wmw", "light_chain_seq": "DIVLTQSPVSLAVSLGQRATISCRASESVDNYGISFMSWFQQKPGQPPKLLIYAASHQGSGVPARFSGSGSGTDFSLNIHPMEEDDSAMYFCLQSKEVPWTFGGGTKLEIKRT", "cdrh1_seq": "GYTFTDYG", "cdrh2_seq": "INTYTGEP", "cdrh3_seq": "ARRYGPEDIDY", "cdrl1_seq": "ESVDNYGISF", "cdrl2_seq": "AAS", "cdrl3_seq": "LQSKEVPWT", "cdrh1_pos": "[24, 31]", "cdrh2_pos": "[49, 56]", "cdrh3_pos": "[95, 105]", "cdrl1_pos": "[26, 35]", "cdrl2_pos": "[53, 55]", "cdrl3_pos": "[92, 100]", "cdrh3_split": "val", "cdrh3_cluster": "6wmw", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "3P10", "antibody_format": "Fab", "heavy_subclass": "IGHV9", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "GDNF family receptor alpha-like, Homo sapiens", "target_domain": null, "functional_role": "other", "evidence_quote": "antagonistic monoclonal antibody that inhibits RET signaling by preventing GDF15-driven interaction of RET with GFRAL"}}}, "tokenized_instruction": [2, 3036, 1920, 27203, 5675, 1958, 1925, 3533, 1988, 2832, 2162, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 11469, 2930, 12, 20733, 1020, 1026, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1925, 11091, 22307, 3416, 3148, 4595, 17, 3189, 12, 15316, 1923, 13, 1927, 16350, 27974, 18, 15316, 1923, 1977, 43, 14938, 17, 6715, 3148, 1958, 1920, 25541, 3962, 6365, 1988, 11847, 1925, 21029, 2644, 1930, 10412, 25541, 3962, 17, 2719, 22009, 1930, 2936, 1927, 1920, 3172, 6941, 4016, 3148, 16, 4523, 1942, 2936, 1927, 7859, 1930, 5496, 3197, 3873, 1930, 2294, 1927, 2628, 3286, 1922, 4486, 4714, 18, 1920, 3533, 1977, 4609, 1942, 28104, 1920, 25541, 3962, 17, 15316, 1923, 17, 3172, 3197, 5432, 2007, 8444, 25541, 3962, 17, 6446, 2835, 1927, 3172, 1956, 15316, 1923, 16, 6113, 26526, 2539, 27541, 18, 3], "antigen": ["WSCLEVAEACVGDVVCNAQLASYLKACSANGNPCDLKQCQAAIRFFYQNIPFNIAQMLAFCDCAQSDIPCQQSKEALHSKTCAVNMVPPPTCLSVIRSCQNDELCRRHYRTFQSKCWQRVTRKCHEDENCISTLSKQDLTCSGSDDCKAAYIDILGTVLQVQCTCRTITQSEESLCKIFQHMLHRKSCFNYP"]} {"modality_type": "antibody", "text": "What would be the HCDR sequences of an antibody with the following function: A human Fab, S309 (IGHV1/IGKV3-Kappa), targeting the Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (BA.2.75 variant). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host ACE2 receptor and mediates fusion of viral and cellular membranes through conformational changes. The antibody is designed as a neutralizing antibody targeting a conserved epitope on the Spike glycoprotein that is broadly recognized across sarbecoviruses and maintains activity against immune-evasive variants.", "target_protein": "QVQLVQSGAEVKKPGASVKVSCKASISWVRQAPGQGLEWMGWNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCWGQGTLVGYPFTSYGISTYNGNTARDYTRGAWFGESLIGGFDN", "metadata": {"pdb_id": "7yqy", "light_chain_seq": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKR", "cdrh1_seq": "GYPFTSYG", "cdrh2_seq": "ISTYNGNT", "cdrh3_seq": "ARDYTRGAWFGESLIGGFDN", "cdrl1_seq": "QTVSSTS", "cdrl2_seq": "GAS", "cdrl3_seq": "QQHDTSLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 115]", "cdrl1_pos": "[26, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9lbs", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV1", "light_subclass": "IGKV3", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "S309 recovered its binding activity against BA.2.75 RBD and exhibited slightly improved neutralization activity"}}}, "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 27203, 1005, 3709, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 7390, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 16, 5133, 1920, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 6813, 18, 22, 18, 4089, 6031, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 8298, 1028, 3148, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 5133, 43, 5305, 10095, 1990, 1920, 10429, 11424, 1988, 1977, 11984, 6783, 3436, 9851, 12409, 18368, 1930, 16566, 2455, 3316, 3743, 17, 2180, 13130, 1961, 4936, 18, 3], "antigen": ["TQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHENNKSRMESELRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPVNLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSSWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFHEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPE"]} {"modality_type": "antibody", "text": "I am designing an antibody with the following function: A human Fab, S2L20 (IGHV3/IGKV1-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2. The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes through conformational changes and proteolytic cleavage. The antibody is designed to function as a membrane-anchored receptor mimic that promotes viral entry and membrane fusion by binding the N-terminal domain (NTD) and inducing RBD opening and exposure of the S2' cleavage site. Please generate the HCDRs for this antibody.", "target_protein": "EVQLVESGGGVVQPGGSLRLSCAASMHWVRQAPGKGLEWVAFYYADSVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCWGQGTLVTVSGFTFNSYGIRYDGGNKANLKDSRYSGSYYDY", "metadata": {"pdb_id": "9c45", "light_chain_seq": "VIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKVDFK", "cdrh1_seq": "GFTFNSYG", "cdrh2_seq": "IRYDGGNK", "cdrh3_seq": "ANLKDSRYSGSYYDY", "cdrl1_seq": "QDIRFY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYDNLPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9c44", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S2L20", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "N-terminal domain (NTD)", "functional_role": "other", "evidence_quote": "S2L20-CVR acts as a functional receptor for SARS-CoV-2, supporting membrane fusion, pseudovirus entry, and authentic virus infection"}}}, "tokenized_instruction": [2, 51, 2150, 14246, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 5159, 11232, 1008, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 1930, 12712, 6404, 18, 1920, 3533, 1977, 4609, 1942, 2347, 1966, 43, 3260, 17, 17199, 3148, 10223, 1988, 7383, 4324, 6904, 1930, 3260, 5289, 2007, 2743, 1920, 56, 17, 4262, 3418, 12, 22078, 13, 1930, 7834, 25780, 9497, 1930, 3395, 1927, 1920, 5159, 11, 6404, 3200, 18, 11586, 5655, 1920, 27203, 5675, 1958, 2052, 3533, 18, 3], "antigen": ["QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHSWMESEFRVYSSANNCTFEYVSQPFLFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSF"]} {"modality_type": "antibody", "text": "A human Fab, atezolizumab (IGHV3/IGKV1-Kappa), targeting the engineered Ig-like V-type domain of Programmed cell death 1 ligand 1 (PD-L1). PD-L1 plays a critical role in induction and maintenance of immune tolerance by binding the inhibitory receptor PD-1 on T cells; tumors exploit this pathway to attenuate anti-tumor immunity. The antibody is designed to block the PD-1/PD-L1 interaction by outcompeting PD-1 for binding to PD-L1, thereby reversing T-cell exhaustion and restoring anti-tumor immune responses. The above text is a description of the function of my antibody. What HCDRs correspond to this functional description?", "target_protein": "EVQLVESGGGLVQPGGSLRLSCAASIHWVRQAPGKGLEWVAWYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCWGQGTLVTVSSAGFTFSDSWISPYGGSTARRHWPGGFDY", "metadata": {"pdb_id": "5x8l", "light_chain_seq": "DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYHPATFGQGTKVEIKRT", "cdrh1_seq": "GFTFSDSW", "cdrh2_seq": "ISPYGGST", "cdrh3_seq": "ARRHWPGGFDY", "cdrl1_seq": "QDVSTA", "cdrl2_seq": "SAS", "cdrl3_seq": "QQYLYHPAT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 106]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "5xxy", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "atezolizumab", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": true, "target_antigen": "Programmed cell death 1 ligand 1, Homo sapiens", "target_domain": "Ig-like V-type", "functional_role": "other", "evidence_quote": "anti-PD-L1 antibodies block the PD-1/PD-L1 interaction by outcompeting PD-1 for binding to PD-L1"}}}, "tokenized_instruction": [2, 43, 2616, 6914, 16, 30280, 13642, 12191, 19240, 3368, 1014, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 7021, 17, 3189, 64, 17, 2601, 3418, 1927, 13839, 2024, 3539, 21, 5207, 21, 12, 3203, 17, 7554, 13, 18, 3203, 17, 7554, 5705, 43, 4140, 2770, 1922, 4408, 1930, 6291, 1927, 3743, 6555, 2007, 2743, 1920, 5431, 3148, 3203, 17, 21, 1990, 62, 2094, 31, 3861, 19443, 2052, 3374, 1942, 15500, 2246, 17, 2798, 7611, 18, 1920, 3533, 1977, 4609, 1942, 3367, 1920, 3203, 17, 21, 19, 3203, 17, 7554, 2835, 2007, 2986, 4617, 6649, 3203, 17, 21, 1958, 2743, 1942, 3203, 17, 7554, 16, 6113, 26526, 62, 17, 2024, 19889, 1930, 20174, 2246, 17, 2798, 3743, 3387, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 3533, 18, 4663, 27203, 5675, 5593, 1942, 2052, 3183, 8418, 35, 3], "antigen": ["AFTVTVPKDLYVVEYGSNMTIECKFPVEKELDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAP"]} {"modality_type": "antibody", "text": "Generate the HCDR loops for an antibody with the following function: A human Fab, S309 (IGHV3/IGKV1-Kappa), targeting the engineered Spike glycoprotein of Severe acute respiratory syndrome coronavirus 2 (Omicron variant B.1.1.529). The Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptors and mediates fusion of viral and cellular membranes through conformational changes triggered by receptor binding or proteolytic cleavage. The antibody is designed as a broadly neutralizing sarbecovirus antibody, binding within the N-terminal domain (NTD).", "target_protein": "EVQLVESGGGVVQPGGSLRLSCAASMHWVRQAPGKGLEWVAFKYYASVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCWGQGTLVTVSGFTFNSYGIRYDGGNANLKDSRYSGSYYDY", "metadata": {"pdb_id": "7tlz", "light_chain_seq": "VIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKV", "cdrh1_seq": "GFTFNSYG", "cdrh2_seq": "IRYDGGN", "cdrh3_seq": "ANLKDSRYSGSYYDY", "cdrl1_seq": "QDIRFY", "cdrl2_seq": "DAS", "cdrl3_seq": "QQYDNLPFT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 56]", "cdrh3_pos": "[95, 109]", "cdrl1_pos": "[26, 31]", "cdrl2_pos": "[49, 51]", "cdrl3_pos": "[88, 96]", "cdrh3_split": "val", "cdrh3_cluster": "9c44", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "S309", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Spike glycoprotein, Severe acute respiratory syndrome coronavirus 2", "target_domain": "N-terminal domain (NTD)", "functional_role": "neutralizing", "evidence_quote": "broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309"}}}, "tokenized_instruction": [2, 5655, 1920, 27203, 1005, 11109, 1958, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 6080, 13192, 12, 20733, 1020, 1010, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11091, 10429, 11424, 1927, 4010, 3939, 5481, 4741, 5548, 10703, 22, 12, 7254, 1935, 2830, 6031, 44, 18, 21, 18, 21, 18, 4764, 1026, 13, 18, 1920, 10429, 11424, 5823, 1918, 1920, 19230, 1942, 1920, 2024, 3260, 2007, 8615, 1956, 4423, 4086, 1930, 10412, 5289, 1927, 4324, 1930, 3689, 5726, 2596, 8523, 2840, 9436, 2007, 3148, 2743, 2014, 12712, 6404, 18, 1920, 3533, 1977, 4609, 1966, 43, 11984, 12130, 9851, 12409, 7414, 3533, 16, 2743, 2651, 1920, 56, 17, 4262, 3418, 12, 22078, 13, 18, 3], "antigen": ["QCVNLRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKEFRVYSSANNCTFEYVSQPFLFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSF"]} {"modality_type": "antibody", "text": "Return only the raw HCDR sequences for an antibody with function: A human Fab (IGHV3/IGKV3-Kappa) targeting the engineered Factor H binding protein of Neisseria meningitidis. Factor H binding protein is a bacterial surface lipoprotein that binds human complement factor H to evade complement-mediated lysis; this binding contributes to meningococcal pathogenesis and is a target of vaccine-induced antibodies. The antibody is designed to enhance Factor H binding to FHbp through allosteric modulation of the FH binding site, stabilizing conformational states that favor Factor H engagement.", "target_protein": "QVQLVESGGGLVQPGGSLRLSCVTSMTWVRQAPGKGLEWVSSKYADSVKGRLTISRDDSMDTLYLQMNSLRAEDTAIYYCWGRGTLVTVSSAGFTFRSYAISHSGGSTAKDQISYPAASPLDY", "metadata": {"pdb_id": "7ket", "light_chain_seq": "IVLTQSPGTLSLSPGERATLSCRASFSLAWYQQKPGQAPRLLIYAPSNRATGIADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPITFGQGTRLEIKRT", "cdrh1_seq": "GFTFRSYA", "cdrh2_seq": "ISHSGGST", "cdrh3_seq": "AKDQISYPAASPLDY", "cdrl1_seq": "FSL", "cdrl2_seq": "APS", "cdrl3_seq": "QQYGSSPIT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[25, 27]", "cdrl2_pos": "[44, 46]", "cdrl3_pos": "[83, 91]", "cdrh3_split": "val", "cdrh3_cluster": "7ket", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": null, "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV3", "is_engineered": true, "target_antigen": "Factor H binding protein, Neisseria meningitidis", "target_domain": null, "functional_role": "other", "evidence_quote": "human Fabs enhance FH binding through structural rearrangement in a region of FHbp adjacent to the FH binding site"}}}, "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 27203, 1005, 3709, 1958, 1925, 3533, 1956, 2347, 30, 43, 2616, 6914, 12, 20733, 1020, 1010, 19, 7021, 1040, 1020, 1010, 17, 12093, 13, 5133, 1920, 11091, 2991, 50, 2743, 2213, 1927, 28356, 18339, 10286, 24977, 18, 2991, 50, 2743, 2213, 1977, 43, 4543, 3154, 9694, 1988, 6876, 2616, 5508, 2991, 50, 1942, 28917, 5508, 17, 3434, 8502, 31, 2052, 2743, 7624, 1942, 10286, 11748, 6559, 1930, 1977, 43, 2758, 1927, 5955, 17, 2719, 3788, 18, 1920, 3533, 1977, 4609, 1942, 4826, 2991, 50, 2743, 1942, 11912, 3846, 2596, 14772, 7145, 1927, 1920, 11912, 2743, 3200, 16, 14384, 8523, 4376, 1988, 7197, 2991, 50, 9577, 18, 3], "antigen": ["GLADALTAPLDHKDKGLQSLTLDQSVRKNEKLKLAAQGAEKTYGNGDSLNTGKLKNDKVSRFDFIRQIEVDGQLITLESGEFQVYKQSHSALTAFQTEQIQDSEHSGKMVAKRQFRIGDIAGEHTSFDKLPEGGRATYRGTAFGSDDAGGKLTYTIDFAAKQGNGKIEHLKSPELNVDLAAADIKPDGKRHAVISGSVLYNQAEKGSYSLGIFGGKAQEVAGSAEVKTVNGIRHIGLAAKQL"]} {"modality_type": "antibody", "text": "I want to design an antibody that has the following function: A human Fab, MR78 (IGHV4/IGKV1-Kappa), targeting the Envelope glycoprotein GP1 of Lake Victoria marburgvirus (strain Ravn-87). GP1 is responsible for binding to cellular receptors CD209 and CLEC4M, which facilitate infection of macrophages and endothelial cells. The antibody is designed as a neutralizing antibody that blocks NPC1 receptor binding and recognizes a conserved epitope at the apex of GP1 that overlaps the receptor-binding site, accessible on the viral surface of Marburg virus. Please generate its HCDRs.", "target_protein": "QLQLQESGPGLVKPSETLSLTCTVSWGWIRQPPGKGLEWIGSSYNPSLKSRATISVDTSKNQFSLNLDSVSAADTAIYYCWGKGSTVTVSSAGGSISSSSYYVYYSGGAASIYGSGTFYYYFYMDV", "metadata": {"pdb_id": "5uqy", "light_chain_seq": "IQMTQSPSSLSASVGDRVTITCQASQVISNYLNWYQQKPGKAPKLLIYDTSNLKTGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYENLQFTFGPGTKVDIKRT", "cdrh1_seq": "GGSISSSSYY", "cdrh2_seq": "VYYSGGA", "cdrh3_seq": "ASIYGSGTFYYYFYMDV", "cdrl1_seq": "QVISNY", "cdrl2_seq": "DTS", "cdrl3_seq": "QQYENLQFT", "cdrh1_pos": "[25, 34]", "cdrh2_pos": "[52, 58]", "cdrh3_pos": "[97, 113]", "cdrl1_pos": "[25, 30]", "cdrl2_pos": "[48, 50]", "cdrl3_pos": "[87, 95]", "cdrh3_split": "val", "cdrh3_cluster": "5uqy", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "MR78", "antibody_format": "Fab", "heavy_subclass": "IGHV4", "light_subclass": "IGKV1", "is_engineered": false, "target_antigen": "Envelope glycoprotein GP1, Lake Victoria marburgvirus (strain Ravn-87)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "MR78 neutralizes authentic MARV and blocks binding of the essential NPC1 receptor domain C"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2258, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 2852, 7950, 12, 20733, 1020, 1006, 19, 7021, 1040, 7390, 17, 12093, 13, 16, 5133, 1920, 11262, 11424, 4882, 1009, 1927, 13296, 25980, 3684, 14020, 11074, 12, 3943, 23624, 1022, 17, 5783, 13, 18, 4882, 1009, 1977, 5061, 1958, 2743, 1942, 3689, 4086, 16494, 1026, 1930, 2965, 17875, 1035, 16, 2154, 6628, 2909, 1927, 5205, 1930, 5003, 2094, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 29653, 3148, 2743, 1930, 16197, 43, 5305, 10095, 2019, 1920, 14091, 1927, 4882, 1009, 1988, 19853, 1920, 3148, 17, 2743, 3200, 16, 10551, 1990, 1920, 4324, 3154, 1927, 3684, 14020, 3413, 18, 11586, 5655, 2496, 27203, 5675, 18, 3], "antigen": ["VCSGTLQKTEDVHLMGFTLSGQKVADSPLEASKRWAFRTGVPPKNVEYTEGEEAKTCYNISVTDPSGKSLLLDPPSNIRDYPKCKTVHHIQGQNPHAQGIALHLWGAFFLYDRVASTTMYRGKVFTEGNIAAMIVNKTVHRMIFS"]} {"modality_type": "antibody", "text": "Give me the HCDR sequences that can form the binding loops of an antibody with the following function: A human Fab, DENV-290 (IGHV3/IGKV2-Kappa), targeting the Genome polyprotein (Envelope protein) of Dengue virus type 3. The Envelope protein mediates viral attachment and fusion during infection. The antibody is designed as a neutralizing antibody that blocks virus attachment to cells, defining a new class of EDE-C epitope that spans the center of the E protein dimer across domain II of two opposite protomers.", "target_protein": "QVELVESGGDVVQPGKSLRLSCAASMHWLRQAPGKGLEWVAVYYADSVKGRFTISRDNSKNTLYLQMNSLTPEDTAVYYCWGQGTLVTVSSGFTFTNYAISSDVNDKAREQAVGTNPWAFDY", "metadata": {"pdb_id": "8jn6", "light_chain_seq": "IVMTQSPLSLSVTPGQPASISCKSSQISSWGSDGKTYLYWYLQKPGQSPQLLIYEVSSRFSGVSDRFSGSGSGTDFTLKISRVQAEDVGLYYCMQGLHLPLTFGQGTRLEIK", "cdrh1_seq": "GFTFTNYA", "cdrh2_seq": "ISSDVNDK", "cdrh3_seq": "AREQAVGTNPWAFDY", "cdrl1_seq": "QISSWGSDGKTY", "cdrl2_seq": "EVS", "cdrl3_seq": "MQGLHLPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[25, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "8jn4", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DENV-290", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Genome polyprotein (Envelope protein), Dengue virus type 3", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "ultrapotent against dengue virus 3 strains; potently neutralize DENV3 with PRNT50 values in the nanogram/mL range"}}}, "tokenized_instruction": [2, 7031, 2142, 1920, 27203, 1005, 3709, 1988, 2112, 2386, 1920, 2743, 11109, 1927, 1925, 3533, 1956, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 14262, 17, 19029, 12, 20733, 1020, 1010, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 3843, 6240, 5684, 12, 11262, 2213, 13, 1927, 13304, 3413, 2601, 23, 18, 1920, 11262, 2213, 10412, 4324, 8576, 1930, 5289, 2409, 2909, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 7644, 3413, 8576, 1942, 2094, 16, 11266, 43, 2814, 2921, 1927, 3347, 1021, 17, 45, 10095, 1988, 23658, 1920, 4102, 1927, 1920, 47, 2213, 7632, 3436, 3418, 2890, 1927, 2288, 8179, 23583, 27306, 18, 3], "antigen": ["MRCVGVGNRDFVEGLSGATWVDVVLEHGGCVTTMAKNKPTLDIELQKTEATQLATLRKLCIEGKITNITTDSRCPTQGEAILPEEQDQNYVCKHTYVDRGWGNGCGLFGKGSLVTCAKFQCLESIEGKVVQHENLKYTVIITVHTGDQHQVGNETQGVTAEITPQASTVEAILPEYGTLGLECSPRTGLDFNEMILLTMKNKAWMVHRQWFFDLPLPWTSGATTETPTWNRKELLVTFKNAHAKKQEVVVLGSQEGAMHTALTGATEIQNSGGTSIFAGHLKCRLKMDKLELKGMSYAMCLNTFVLKKEVSETQHGTILIKVEYKGEDAPCKIPFSTEDGQGKAHNGRLITANPVVTKKEEPVNIEAEPPFGESNIVIGIGDKALKINWYKKGS"]} {"modality_type": "antibody", "text": "I want to design an antibody that can perform the following function: A human Fab, DENV-290 (IGHV3/IGKV2-Kappa), targeting the Genome polyprotein (Envelope protein) of dengue virus type 3. The Envelope protein mediates viral attachment and membrane fusion during infection. The antibody is designed as a neutralizing antibody that primarily blocks virus attachment to cells, defining a new class of EDE-C epitope that spans the center of the E protein dimer across domain II of two opposite protomers. Please output the HCDRs.", "target_protein": "QVELVESGGDVVQPGKSLRLSCAASMHWLRQAPGKGLEWVAVYYADSVKGRFTISRDNSKNTLYLQMNSLTPEDTAVYYCWGQGTLVTVSSGFTFTNYAISSDVNDKAREQAVGTNPWAFDY", "metadata": {"pdb_id": "8jn7", "light_chain_seq": "IVMTQSPLSLSVTPGQPASISCKSSQISSWGSDGKTYLYWYLQKPGQSPQLLIYEVSSRFSGVSDRFSGSGSGTDFTLKISRVQAEDVGLYYCMQGLHLPLTFGQGTRLEIK", "cdrh1_seq": "GFTFTNYA", "cdrh2_seq": "ISSDVNDK", "cdrh3_seq": "AREQAVGTNPWAFDY", "cdrl1_seq": "QISSWGSDGKTY", "cdrl2_seq": "EVS", "cdrl3_seq": "MQGLHLPLT", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 110]", "cdrl1_pos": "[25, 36]", "cdrl2_pos": "[54, 56]", "cdrl3_pos": "[93, 101]", "cdrh3_split": "val", "cdrh3_cluster": "8jn4", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "DENV-290", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGKV2", "is_engineered": false, "target_antigen": "Genome polyprotein (Envelope protein), dengue virus type 3", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "ultrapotent against dengue virus 3 strains; potently neutralize DENV3 with PRNT50 values in the nanogram/mL range"}}}, "tokenized_instruction": [2, 51, 12914, 1942, 3036, 1925, 3533, 1988, 2112, 2385, 1920, 2894, 2347, 30, 43, 2616, 6914, 16, 14262, 17, 19029, 12, 20733, 1020, 1010, 19, 7021, 1040, 15755, 17, 12093, 13, 16, 5133, 1920, 3843, 6240, 5684, 12, 11262, 2213, 13, 1927, 13304, 3413, 2601, 23, 18, 1920, 11262, 2213, 10412, 4324, 8576, 1930, 3260, 5289, 2409, 2909, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 5985, 7644, 3413, 8576, 1942, 2094, 16, 11266, 43, 2814, 2921, 1927, 3347, 1021, 17, 45, 10095, 1988, 23658, 1920, 4102, 1927, 1920, 47, 2213, 7632, 3436, 3418, 2890, 1927, 2288, 8179, 23583, 27306, 18, 11586, 6647, 1920, 27203, 5675, 18, 3], "antigen": ["MRCVGVGNRDFVEGLSGATWVDVVLEHGGCVTTMAKNKPTLDIELQKTEATQLATLRKLCIEGKITNITTDSRCPTQGEAILPEEQDQNYVCKHTYVDRGWGNGCGLFGKGSLVTCAKFQCLESIEGKVVQHENLKYTVIITVHTGDQHQVGNETQGVTAEITPQASTVEAILPEYGTLGLECSPRTGLDFNEMILLTMKNKAWMVHRQWFFDLPLPWTSGATTETPTWNRKELLVTFKNAHAKKQEVVVLGSQEGAMHTALTGATEIQNSGGTSIFAGHLKCRLKMDKLELKGMSYAMCLNTFVLKKEVSETQHGTILIKVEYKGEDAPCKIPFSTEDGQGKAHNGRLITANPVVTKKEEPVNIEAEPPFGESNIVIGIGDKALKINWYKKGS"]} {"modality_type": "antibody", "text": "The antibody I want to design has this role: A human Fab, G9E (IGHV3/IGLV2-Lambda), targeting the E protein of Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013). The E protein is a surface glycoprotein that mediates viral attachment and entry into host cells. The antibody is designed as a neutralizing antibody that cross-links E protein homodimers to prevent the low pH-triggered conformational changes required for viral membrane fusion and genome release during endosomal entry. What would the HCDRs be?", "target_protein": "RVHLVESGGGVVQPGRSLRLSCVASMHWVRQAPGKGLEWVAIYYADSVKGRFTISRDNSKNTLFLQMNRLRAEDTALYYCWGQGTLVTVSSAGFAFSNYHIWDDGSDQVGGSSAYNGDNGWREAASLDD", "metadata": {"pdb_id": "7yar", "light_chain_seq": "SALTQPASVSGSPGQSITIFCSGSSNDVGGYNYVSWYQQYPGKVPKLLIYDVNSRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSRRTWVFGGGTIVTVLGQ", "cdrh1_seq": "GFAFSNYH", "cdrh2_seq": "IWDDGSDQ", "cdrh3_seq": "VGGSSAYNGDNGWREAASLDD", "cdrl1_seq": "SNDVGGYNY", "cdrl2_seq": "DVN", "cdrl3_seq": "SSYTSRRTWV", "cdrh1_pos": "[25, 32]", "cdrh2_pos": "[50, 57]", "cdrh3_pos": "[96, 116]", "cdrl1_pos": "[24, 32]", "cdrl2_pos": "[50, 52]", "cdrl3_pos": "[89, 98]", "cdrh3_split": "val", "cdrh3_cluster": "7yar", "design_blueprint_metadata": {"extracted_parameters": {"antibody_name": "G9E", "antibody_format": "Fab", "heavy_subclass": "IGHV3", "light_subclass": "IGLV2", "is_engineered": false, "target_antigen": "E protein, Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)", "target_domain": null, "functional_role": "neutralizing", "evidence_quote": "antibody blocks infection by cross-linking and paralyzing proteins on the viral surface required for the virus to enter cells"}}}, "tokenized_instruction": [2, 1920, 3533, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 43, 2616, 6914, 16, 25129, 1021, 12, 20733, 1020, 1010, 19, 28961, 15755, 17, 18279, 13, 16, 5133, 1920, 47, 2213, 1927, 28593, 3413, 12, 9158, 17359, 19, 2616, 19, 12941, 15176, 7156, 19, 2813, 8851, 1034, 1038, 19, 3871, 13, 18, 1920, 47, 2213, 1977, 43, 3154, 11424, 1988, 10412, 4324, 8576, 1930, 6904, 2460, 4423, 2094, 18, 1920, 3533, 1977, 4609, 1966, 43, 12130, 3533, 1988, 3567, 17, 10069, 47, 2213, 29227, 1942, 4625, 1920, 2330, 2087, 17, 9436, 8523, 2840, 3414, 1958, 4324, 3260, 5289, 1930, 3843, 4012, 2409, 16514, 6904, 18, 4663, 2962, 1920, 27203, 5675, 1998, 35, 3], "antigen": ["IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTAVSA"]}