File size: 9,530 Bytes
52007f8 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 | <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 Design -->
<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> |