| <ROSETTASCRIPTS> |
| <SCOREFXNS> |
| <ScoreFunction name="sfxn_soft" weights="beta_nov16_soft" /> |
| <ScoreFunction name="sfxn" weights="beta_nov16" /> |
| <ScoreFunction name="sfxn_relax" weights="beta_nov16" > |
| <Reweight scoretype="arg_cation_pi" weight="3" /> |
| <Reweight scoretype="approximate_buried_unsat_penalty" weight="5" /> |
| <Set approximate_buried_unsat_penalty_burial_atomic_depth="3.5" /> |
| <Set approximate_buried_unsat_penalty_hbond_energy_threshold="-0.5" /> |
| </ScoreFunction> |
| <ScoreFunction name="sfxn_softish" weights="beta_nov16" > |
| <Reweight scoretype="fa_rep" weight="0.15" /> |
| </ScoreFunction> |
| <ScoreFunction name="sfxn_fa_atr" weights="empty" > |
| <Reweight scoretype="fa_atr" weight="1" /> |
| </ScoreFunction> |
| <ScoreFunction name="vdw_sol" weights="empty" > |
| <Reweight scoretype="fa_atr" weight="1.0" /> |
| <Reweight scoretype="fa_rep" weight="0.55" /> |
| <Reweight scoretype="fa_sol" weight="1.0" /> |
| </ScoreFunction> |
| |
| </SCOREFXNS> |
| <RESIDUE_SELECTORS> |
| <Chain name="chainA" chains="A"/> |
| <Chain name="chainB" chains="B"/> |
| <Neighborhood name="interface_chA" selector="chainB" distance="8.0" /> |
| <Neighborhood name="interface_chB" selector="chainA" distance="8.0" /> |
| <And name="AB_interface" selectors="interface_chA,interface_chB" /> |
| <Not name="Not_interface" selector="AB_interface" /> |
| <And name="actual_interface_chB" selectors="AB_interface,chainB" /> |
| <And name="not_interface_chB" selectors="Not_interface,chainB" /> |
|
|
| <ResidueName name="apolar" residue_name3="ALA,CYS,PHE,ILE,LEU,MET,THR,PRO,VAL,TRP,TYR" /> |
| <Not name="polar" selector="apolar" /> |
|
|
| <True name="all" /> |
|
|
| <ResidueName name="pro_and_gly_positions" residue_name3="PRO,GLY" /> |
|
|
| <ResiduePDBInfoHasLabel name="HOTSPOT_res" property="HOTSPOT" /> |
| </RESIDUE_SELECTORS> |
|
|
|
|
| <RESIDUE_SELECTORS> |
| |
| <Layer name="surface" select_core="false" select_boundary="false" select_surface="true" use_sidechain_neighbors="true"/> |
| <Layer name="boundary" select_core="false" select_boundary="true" select_surface="false" use_sidechain_neighbors="true"/> |
| <Layer name="core" select_core="true" select_boundary="false" select_surface="false" use_sidechain_neighbors="true"/> |
| <SecondaryStructure name="sheet" overlap="0" minH="3" minE="2" include_terminal_loops="false" use_dssp="true" ss="E"/> |
| <SecondaryStructure name="entire_loop" overlap="0" minH="3" minE="2" include_terminal_loops="true" use_dssp="true" ss="L"/> |
| <SecondaryStructure name="entire_helix" overlap="0" minH="3" minE="2" include_terminal_loops="false" use_dssp="true" ss="H"/> |
| <And name="helix_cap" selectors="entire_loop"> |
| <PrimarySequenceNeighborhood lower="1" upper="0" selector="entire_helix"/> |
| </And> |
| <And name="helix_start" selectors="entire_helix"> |
| <PrimarySequenceNeighborhood lower="0" upper="1" selector="helix_cap"/> |
| </And> |
| <And name="helix" selectors="entire_helix"> |
| <Not selector="helix_start"/> |
| </And> |
| <And name="loop" selectors="entire_loop"> |
| <Not selector="helix_cap"/> |
| </And> |
|
|
| </RESIDUE_SELECTORS> |
|
|
| <TASKOPERATIONS> |
| <DesignRestrictions name="layer_design_no_core_polars"> |
| <Action selector_logic="surface AND helix_start" aas="DEHKPQR"/> |
| <Action selector_logic="surface AND helix" aas="EHKQR"/> |
| <Action selector_logic="surface AND sheet" aas="EHKNQRST"/> |
| <Action selector_logic="surface AND loop" aas="DEGHKNPQRST"/> |
| <Action selector_logic="boundary AND helix_start" aas="ADEHIKLNPQRSTVWY"/> |
| <Action selector_logic="boundary AND helix" aas="ADEHIKLNQRSTVWY"/> |
| <Action selector_logic="boundary AND sheet" aas="DEFHIKLNQRSTVWY"/> |
| <Action selector_logic="boundary AND loop" aas="ADEFGHIKLNPQRSTVWY"/> |
| <Action selector_logic="core AND helix_start" aas="AFILMPVWY"/> |
| <Action selector_logic="core AND helix" aas="AFILVWY"/> |
| <Action selector_logic="core AND sheet" aas="FILVWY"/> |
| <Action selector_logic="core AND loop" aas="AFGILPVWY"/> |
| <Action selector_logic="helix_cap" aas="DNST"/> |
| </DesignRestrictions> |
| </TASKOPERATIONS> |
|
|
|
|
| <TASKOPERATIONS> |
| <ProteinProteinInterfaceUpweighter name="upweight_interface" interface_weight="3" /> |
| <ProteinInterfaceDesign name="pack_long" design_chain1="0" design_chain2="0" jump="1" interface_distance_cutoff="15"/> |
| <InitializeFromCommandline name="init" /> |
| <IncludeCurrent name="current" /> |
| <LimitAromaChi2 name="limitchi2" chi2max="110" chi2min="70" include_trp="True" /> |
| <ExtraRotamersGeneric name="ex1_ex2" ex1="1" ex2="1" /> |
|
|
|
|
| <OperateOnResidueSubset name="restrict_target_not_interface" selector="not_interface_chB"> |
| <PreventRepackingRLT/> |
| </OperateOnResidueSubset> |
| <OperateOnResidueSubset name="restrict2repacking" selector="all"> |
| <RestrictToRepackingRLT/> |
| </OperateOnResidueSubset> |
| <OperateOnResidueSubset name="restrict_to_interface" selector="Not_interface"> |
| <PreventRepackingRLT/> |
| </OperateOnResidueSubset> |
| <OperateOnResidueSubset name="restrict_target2repacking" selector="chainB"> |
| <RestrictToRepackingRLT/> |
| </OperateOnResidueSubset> |
| <OperateOnResidueSubset name="restrict_hotspots2repacking" selector="HOTSPOT_res"> |
| <RestrictToRepackingRLT/> |
| </OperateOnResidueSubset> |
|
|
| <DisallowIfNonnative name="disallow_GLY" resnum="0" disallow_aas="G" /> |
| <DisallowIfNonnative name="disallow_PRO" resnum="0" disallow_aas="P" /> |
| <SelectBySASA name="PR_monomer_core" mode="sc" state="monomer" probe_radius="2.2" core_asa="10" surface_asa="10" core="0" boundary="1" surface="1" verbose="0" /> |
|
|
| <OperateOnResidueSubset name="restrict_PRO_GLY" selector="pro_and_gly_positions"> |
| <PreventRepackingRLT/> |
| </OperateOnResidueSubset> |
|
|
| PruneBadRotamers name="prune_bad_rotamers" probability_cut="0.01" /> |
|
|
| </TASKOPERATIONS> |
| <MOVERS> |
|
|
|
|
| <SwitchChainOrder name="chain1onlypre" chain_order="1" /> |
| <ScoreMover name="scorepose" scorefxn="sfxn" verbose="false" /> |
| <ParsedProtocol name="chain1only"> |
| <Add mover="chain1onlypre" /> |
| <Add mover="scorepose" /> |
| </ParsedProtocol> |
| <TaskAwareMinMover name="min" scorefxn="sfxn" bb="0" chi="1" task_operations="pack_long" /> |
|
|
| <DeleteRegionMover name="delete_polar" residue_selector="polar" rechain="false" /> |
|
|
|
|
| </MOVERS> |
| <FILTERS> |
| |
| <Time name="timed"/> |
|
|
| <Sasa name="interface_buried_sasa" confidence="0" /> |
| <Ddg name="ddg" threshold="0" jump="1" repeats="1" repack="1" relax_mover="min" confidence="0" scorefxn="sfxn" /> |
| <Ddg name="ddg_norepack" threshold="0" jump="1" repeats="1" repack="0" relax_mover="min" confidence="0" scorefxn="sfxn" /> |
| <ShapeComplementarity name="interface_sc" verbose="0" min_sc="0.55" write_int_area="1" write_median_dist="1" jump="1" confidence="0"/> |
|
|
| |
| ### score function monomer terms |
| <ScoreType name="total_score_MBF" scorefxn="sfxn" score_type="total_score" threshold="0" confidence="0" /> |
| <MoveBeforeFilter name="total_score_monomer" mover="chain1only" filter="total_score_MBF" confidence="0" /> |
| <ResidueCount name="res_count_MBF" max_residue_count="9999" confidence="0"/> |
| <MoveBeforeFilter name="res_count_monomer" mover="chain1only" filter="res_count_MBF" confidence="0" /> |
|
|
| |
| <CalculatorFilter name="score_per_res" equation="total_score_monomer / res" threshold="-3.5" confidence="0"> |
| <Var name="total_score_monomer" filter="total_score_monomer"/> |
| <Var name="res" filter="res_count_monomer"/> |
| </CalculatorFilter> |
|
|
| |
| <InterfaceHydrophobicResidueContacts name="hydrophobic_residue_contacts" target_selector="chainB" binder_selector="chainA" scorefxn="sfxn_soft" confidence="0"/> |
|
|
|
|
| <Ddg name="ddg_hydrophobic_pre" threshold="-10" jump="1" repeats="1" repack="0" confidence="0" scorefxn="vdw_sol" /> |
| <MoveBeforeFilter name="ddg_hydrophobic" mover="delete_polar" filter="ddg_hydrophobic_pre" confidence="0"/> |
|
|
| <ContactMolecularSurface name="contact_molecular_surface" distance_weight="0.5" target_selector="chainA" binder_selector="chainB" confidence="0" /> |
|
|
| </FILTERS> |
|
|
|
|
| <MOVERS> |
|
|
| <FastRelax name="FastRelax" scorefxn="sfxn_relax" repeats="1" batch="false" ramp_down_constraints="false" cartesian="false" bondangle="false" bondlength="false" min_type="dfpmin_armijo_nonmonotone" task_operations="current,ex1_ex2,restrict_target_not_interface,limitchi2" > |
| <MoveMap name="MM" > |
| <Chain number="1" chi="true" bb="true" /> |
| <Chain number="2" chi="true" bb="false" /> |
| <Jump number="1" setting="true" /> |
| </MoveMap> |
| </FastRelax> |
|
|
| </MOVERS> |
| <APPLY_TO_POSE> |
| </APPLY_TO_POSE> |
|
|
| <PROTOCOLS> |
| </PROTOCOLS> |
|
|
| <OUTPUT/> |
| </ROSETTASCRIPTS> |
