bisectgroup/Leak-CURBER-Kd

Leak-CURBER Kd P-seq

Summary

Leak-CURBER is a benchmark for enzymatic reaction tasks (NeurIPS 2026). This repository holds the leaderboard split Kd P-seq at threshold 0.01. It contains the paper's train and validation rows, merged and shuffled with seed 42. The test set is held out for the leaderboard.

Rows

55,748 rows in one train split.

Split

The P-seq split at threshold 0.01: test proteins have a maximum sequence identity to the training proteins below 0.01 (MMseqs2).

Columns

Column	Type	Meaning
smiles	string	SMILES of the ligand (molecule input).
smiles_hash	string	SHA-256 of smiles_key (helper column).
smiles_key	string	Canonical SMILES used for grouping (helper column).
organism	string	Source organism of the target.
sequence	string	Amino acid sequence of the target protein (protein input).
uniprot_id	string	UniProt accession of the target.
value_type	string	Measured quantity (constant in this file).
monomer_id	int64	BindingDB MonomerID (helper column).
ligand	string	Ligand name.
ligand_id	string	Ligand id in the source database (helper column).
target	string	BindingDB target name.
doi	string	DOI of the source article.
pmid	string	PubMed id of the source article.
ligand_target_complex_pdbs	string	PDB ids of ligand-target complexes.
pubchem_cid	string	PubChem compound id.
pubchem_sid	string	PubChem substance id (helper column).
chebi_id	double	ChEBI id.
chembl_id	string	ChEMBL id.
kegg_id	string	KEGG id.
zinc_id	string	ZINC id.
pdbs	list<element: string>	List of PDB ids.
unit	string	Unit of value (mM).
log10_value	double	Target: log10 of value in mM.
value	double	Raw value in mM.
uniprot_date	timestamp[ns]	UniProt entry creation date (helper column; used by the Time split).

Target

log10_value, the log10 of the dissociation constant in mM.

Sources and license

This dataset is released for academic, non-commercial use under CC BY-NC-SA 4.0. The terms of each source database also apply. Users must follow them.

• BindingDB, CC BY 3.0 for staff-curated data (https://www.bindingdb.org/rwd/bind/info.jsp). It includes records that BindingDB imports from ChEMBL, which are CC BY-SA 3.0 (https://chembl.gitbook.io/chembl-interface-documentation/about).
• UniProt, CC BY 4.0 (https://www.uniprot.org/help/license): protein sequences and annotation dates.
• RCSB PDB, CC0 1.0 (https://www.rcsb.org/pages/usage-policy), and AlphaFold DB, CC BY 4.0 (https://alphafold.ebi.ac.uk/faq): structure ids in the pdbs column refer to these databases, where present.

All rows come from BindingDB. The files have no per-row source column, so ChEMBL-imported records cannot be separated.

Citation

@inproceedings{ahmed2026leakcurber,
  title     = {Leak-CURBER: A Leakage-Controlled Multimodal Evaluation Benchmark for Enzymatic Reaction Tasks},
  author    = {Ahmed, Adhil and Balaji, Roshan and Bhatt, Nirav Pravinbhai},
  booktitle = {Advances in Neural Information Processing Systems},
  year      = {2026}
}

Code: https://github.com/bisect-group/Leak-CURBER

Please also cite the sources this dataset uses:

@article{liuBindingDB2024FAIR2025,
    title = {{BindingDB} in 2024: a {FAIR} knowledgebase of protein-small molecule binding data},
    volume = {53},
    issn = {1362-4962},
    url = {https://doi.org/10.1093/nar/gkae1075},
    doi = {10.1093/nar/gkae1075},
    number = {D1},
    journal = {Nucleic Acids Research},
    author = {Liu, Tiqing and Hwang, Linda and Burley, Stephen K and Nitsche, Carmen I and Southan, Christopher and Walters, W Patrick and Gilson, Michael K},
    month = jan,
    year = {2025},
    pages = {D1633--D1644},
}

@article{theuniprotconsortiumUniProtUniversalProtein2025,
    title = {{UniProt}: the {Universal} {Protein} {Knowledgebase} in 2025},
    volume = {53},
    issn = {1362-4962},
    url = {https://doi.org/10.1093/nar/gkae1010},
    doi = {10.1093/nar/gkae1010},
    number = {D1},
    journal = {Nucleic Acids Research},
    author = {{The UniProt Consortium}},
    month = jan,
    year = {2025},
    pages = {D609--D617},
}

@article{armstrongPDBeImprovedFindability2020,
    title = {{PDBe}: improved findability of macromolecular structure data in the {PDB}},
    volume = {48},
    issn = {0305-1048},
    url = {https://doi.org/10.1093/nar/gkz990},
    doi = {10.1093/nar/gkz990},
    number = {D1},
    journal = {Nucleic Acids Research},
    author = {Armstrong, David R and Berrisford, John M and Conroy, Matthew J and Gutmanas, Aleksandras and Anyango, Stephen and Choudhary, Preeti and Clark, Alice R and Dana, Jose M and Deshpande, Mandar and Dunlop, Roisin and Gane, Paul and Gáborová, Romana and Gupta, Deepti and Haslam, Pauline and Koča, Jaroslav and Mak, Lora and Mir, Saqib and Mukhopadhyay, Abhik and Nadzirin, Nurul and Nair, Sreenath and Paysan-Lafosse, Typhaine and Pravda, Lukas and Sehnal, David and Salih, Osman and Smart, Oliver and Tolchard, James and Varadi, Mihaly and Svobodova-Vařeková, Radka and Zaki, Hossam and Kleywegt, Gerard J and Velankar, Sameer},
    month = jan,
    year = {2020},
    pages = {D335--D343},
}

@article{varadiAlphaFoldProteinStructure2024,
    title = {{AlphaFold} {Protein} {Structure} {Database} in 2024: providing structure coverage for over 214 million protein sequences},
    volume = {52},
    issn = {0305-1048},
    url = {https://doi.org/10.1093/nar/gkad1011},
    doi = {10.1093/nar/gkad1011},
    number = {D1},
    journal = {Nucleic Acids Research},
    author = {Varadi, Mihaly and Bertoni, Damian and Magana, Paulyna and Paramval, Urmila and Pidruchna, Ivanna and Radhakrishnan, Malarvizhi and Tsenkov, Maxim and Nair, Sreenath and Mirdita, Milot and Yeo, Jingi and Kovalevskiy, Oleg and Tunyasuvunakool, Kathryn and Laydon, Agata and Žídek, Augustin and Tomlinson, Hamish and Hariharan, Dhavanthi and Abrahamson, Josh and Green, Tim and Jumper, John and Birney, Ewan and Steinegger, Martin and Hassabis, Demis and Velankar, Sameer},
    month = jan,
    year = {2024},
    pages = {D368--D375},
}

@article{zdrazil2023chembl,
  title = {The {ChEMBL} Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods},
  author = {Zdrazil, Barbara and Felix, Eloy and Hunter, Fiona and Manners, Emma J and Blackshaw, James and Corbett, Sybilla and de Veij, Marleen and Ioannidis, Harris and Lopez, David Mendez and Mosquera, Juan F and Magarinos, Maria Paula and Bosc, Nicolas and Arcila, Ricardo and Kizil{\"o}ren, Tevfik and Gaulton, Anna and Bento, A Patr{\'i}cia and Adasme, Melissa F and Monecke, Peter and Landrum, Gregory A and Leach, Andrew R},
  journal = {Nucleic Acids Research},
  volume = {52},
  number = {D1},
  pages = {D1180--D1192},
  year = {2023},
  doi = {10.1093/nar/gkad1004}
}