Side chain rotamer design and filtering protocol
<kappa_peptide_design.xml>
<ROSETTASCRIPTS> 
 
#########################################################################
### This script is meant to design sequence on to a backbone scaffold ###
### in the binding pocket of the protein/receptor of interest.        ### 
#########################################################################
 
    <SCOREFXNS> 
 
        <ScoreFunction name="ref" weights="ref2015"/> 
 
        <ScoreFunction name="ref_cst" weights="ref2015"> 
            <Reweight scoretype="coordinate_constraint" weight="1" /> 
            <Reweight scoretype="atom_pair_constraint" weight="1" /> 
            <Reweight scoretype="dihedral_constraint" weight="1" /> 
            <Reweight scoretype="angle_constraint" weight="1" /> 
        </ScoreFunction> 
 
        <ScoreFunction name="ref_comp" weights="ref2015" > 
            <Reweight scoretype="coordinate_constraint" weight="1" /> 
            <Reweight scoretype="atom_pair_constraint" weight="1" /> 
            <Reweight scoretype="dihedral_constraint" weight="1" /> 
            <Reweight scoretype="angle_constraint" weight="1" /> 
            <Reweight scoretype="aa_composition" weight="1" /> 
        </ScoreFunction>      
 
    </SCOREFXNS> 
 
    <RESIDUE_SELECTORS> 
 
        <Chain name="protein" chains="A"/> 
        <Chain name="peptide" chains="B" />
 
        <Phi name="posPhi" select_positive_phi="true" /> 
        <And name="posPhi_B" selectors="peptide,posPhi" /> 
        <Phi name="negPhi" select_positive_phi="false" /> 
        <And name="negPhi_B" selectors="peptide,negPhi" /> 
 
        <Neighborhood name="interface_chB" selector="peptide" distance="8.0"/> 
        <Neighborhood name="interface_chA" selector="protein" distance="8.0"/> 
        <And name="AB_interface" selectors="interface_chB,interface_chA"/> 
 
        <ResidueName name="stub_sel" residue_name3="CYY,DPH"/> 
 
    </RESIDUE_SELECTORS> 
 
    <TASKOPERATIONS> 
 
        <ReadResfile name="l_res" filename="l_res.txt" selector="negPhi"/> 
        <ReadResfile name="d_res" filename="d_res.txt" selector="posPhi"/> 
 
        <OperateOnResidueSubset name="no_design_stub" selector="stub_sel"> 
            <RestrictToRepackingRLT/> 
        </OperateOnResidueSubset> 
 
        <OperateOnResidueSubset name="only_repack_chain" selector="protein"> 
            <RestrictToRepackingRLT/> 
        </OperateOnResidueSubset> 
 
        <DisallowIfNonnative name="no_cys" disallow_aas="CG"/> 
 
        <OperateOnResidueSubset name="no_repack_except_interface" > 
            <And> 
                <Chain chains="1"/> 
                <Not> 
                    <Neighborhood distance="8.0" > 
                        <Chain chains="2"/> 
                    </Neighborhood> 
                </Not> 
            </And> 
            <PreventRepackingRLT /> 
        </OperateOnResidueSubset> 
 
        <IncludeCurrent name="current"/> 
 
        <OperateOnResidueSubset name="restrict_to_interface" selector="AB_interface"> 
            <RestrictToRepackingRLT/> 
        </OperateOnResidueSubset>  
 
    </TASKOPERATIONS> 
 
    <FILTERS> 
 
        <ScoreType name="score" 
        	scorefxn="ref" 
        	score_type="total_score" 
        	threshold="50" /> 
 
        <ResidueCount name="gly_count" 
        	max_residue_count="2" 
        	min_residue_count="0" 
        	residue_types="GLY" 
        	count_as_percentage="0"/> 
 
        <ShapeComplementarity name="sc_filter" 
        	verbose="0" 
        	write_int_area="1" 
        	jump="1" 
        	confidence="0"/>
 
        <AtomicContactCount name="interface_contactcount" 
        	task_operations="restrict_to_interface" 
        	confidence="0"/> 
         
        <Ddg name="ddg"  
        	threshold="10" 
        	jump="1" 
        	repeats="5" 
        	repack="1" 
        	confidence="1" 
        	scorefxn="ref"/>
 
        <Ddg name="ddg_norepack"  
        	threshold="15" 
        	jump="1" 
        	repeats="1" 
        	repack="0" 
        	confidence="1" 
        	scorefxn="ref"/> 
 
        <Sasa name="interface_buried_sasa" 
        	confidence="0"/> 
 
        <Sasa name="interface_hydrophobic_sasa" 
        	confidence="0" 
        	hydrophobic="True"/> 
 
        <Sasa name="interface_polar_sasa" 
        	confidence="0" 
        	polar="True"/> 
 
        <BuriedUnsatHbonds name="new_buns_bb_heavy"  
        	ignore_surface_res="true" 
        	report_bb_heavy_atom_unsats="true" 
        	scorefxn="ref" 
        	confidence="0" 
        	print_out_info_to_pdb="true" /> 
 
        <BuriedUnsatHbonds name="new_buns_sc_heavy" 
        	ignore_surface_res="true" 
        	report_sc_heavy_atom_unsats="true" 
        	scorefxn="ref" 
        	confidence="0" 
        	print_out_info_to_pdb="true" /> 
  
        <AtomicDistance name="distancefilter" 
        	residue1="288" 
        	atomname1="CZ" 
        	residue2="84" 
        	atomname2="CG1" 
        	distance="8"/> 
 
    </FILTERS> 
 
    <MOVERS>         
 
        <DeclareBond name="bond" res1="286" atom1="CE" res2="282" atom2="N" add_termini="false"/> 
 
        <CreateTorsionConstraint name="peptide_torsion_constraints"> 
            <Add res1="286" res2="286" res3="282" res4="282" atom1="CD" atom2="CE" atom3="N" atom4="CA" cst_func="CIRCULARHARMONIC 3.141592654 0.005"/> 
        </CreateTorsionConstraint> 
 
        <CreateAngleConstraint name="peptide_angle_constraints"> 
            <Add res1="286" atom1="CD" res_center="286" atom_center="CE" res2="282" atom2="N" cst_func="CIRCULARHARMONIC 2.02807247 0.005" /> 
            <Add res1="286" atom1="CE" res_center="282" atom_center="N" res2="282" atom2="CA" cst_func="CIRCULARHARMONIC 2.14675 0.005" /> 
        </CreateAngleConstraint> 
 
        <CreateDistanceConstraint name="distance_constraints"> 
            <Add res1="286" res2="282" atom1="CE" atom2="N" cst_func="HARMONIC 1.33 0.01" /> 
        </CreateDistanceConstraint> 

        <FastDesign name="design" task_operations="d_res,l_res,only_repack_chain, no_repack_except_interface,no_design_stub,no_cys,current" scorefxn="ref_comp" repeats="3" ramp_down_constraints="false"> 
            <MoveMap name="specifics"> 
                <Jump number="1" setting="0" /> 
                <Span begin="1" end="281" chi="0" bb="0"/> 
            </MoveMap> 
        </FastDesign> 
 
<FastRelax name="relax" scorefxn="ref_cst" repeats="2" ramp_down_constraints="false"> 
            <MoveMap name="specifics"> 
                <Jump number="1" setting="0" /> 
                <Span begin="1" end="281" chi="0" bb="0"/> 
            </MoveMap> 
        </FastRelax> 
 
    </MOVERS> 
 
    <APPLY_TO_POSE> 
    </APPLY_TO_POSE> 
 
    <PROTOCOLS> 
 
        <Add mover="bond" /> 
        <Add mover="peptide_torsion_constraints" /> 
        <Add mover="peptide_angle_constraints" /> 
        <Add mover="distance_constraints" />
 
        <Add mover="design"/>
 
        <Add mover="bond" /> 
        <Add mover="peptide_torsion_constraints" /> 
        <Add mover="peptide_angle_constraints" /> 
        <Add mover="distance_constraints" />
 
        <Add mover="relax" />
 
        <Add filter_name="distancefilter"/> 
        <Add filter="new_buns_bb_heavy"/> 
        <Add filter="new_buns_sc_heavy"/> 
    	<Add filter="sc_filter" /> 
    	<Add filter="interface_contactcount"/> 
    	<Add filter="ddg"/> 
    	<Add filter="ddg_norepack"/> 
    	<Add filter="interface_buried_sasa"/> 
    	<Add filter="interface_hydrophobic_sasa"/> 
    	<Add filter="interface_polar_sasa"/> 
 
    </PROTOCOLS> 
 
    <OUTPUT /> 
</ROSETTASCRIPTS>