design disulfide rich peptides

build_and_disulfidize.xml

<ROSETTASCRIPTS>

<!--

keywords:   de novo design, disulfide design
author:     Christopher D. Bahl
email:      [email protected]
url:        http://function-structure.org/

This protocol will design disulfide rich peptides de novo

-->

	<SCOREFXNS>

		<!-- centroid score function used for protein backbone design -->
		<ScoreFunction name="score_design_centroid" weights="fldsgn_cen">
			<Reweight scoretype="cenpack" weight="1.0"/>
			<Reweight scoretype="hbond_sr_bb" weight="1.0"/>
			<Reweight scoretype="hbond_lr_bb" weight="1.0"/>
			<Reweight scoretype="atom_pair_constraint" weight="1.0"/>
			<Reweight scoretype="angle_constraint" weight="1.0"/>
			<Reweight scoretype="dihedral_constraint" weight="1.0"/>
		</ScoreFunction>

		<!-- the current default energy function without additional energy terms -->
		<ScoreFunction name="score_evaluate" weights="ref2015"/>

	</SCOREFXNS>


	<FILTERS>

		<DisulfideEntropy name="disulfide_entropy"/>

		<SheetTopology name="filter_strand_pairing" topology="%%topology%%" blueprint="%%blueprint%%" confidence="1"/>
		<SecondaryStructureCount name="count_SS_elements" filter_helix_sheet="True" num_helix="1" num_sheet="3" num_helix_sheet="4" min_helix_length="5" min_sheet_length="3" min_loop_length="2" confidence="1"/> 
		<CompoundStatement name="compound_toplogy_filter" >
			<AND filter_name="filter_strand_pairing" />
			<AND filter_name="count_SS_elements" />
		</CompoundStatement>

	</FILTERS>


	<MOVERS>

		<!-- assign secondary structure information to the pose -->
		<Dssp name="dssp" />

		<!-- design the protein main chain -->
		<SetSecStructEnergies name="assign_secondary_structure_bonus" scorefxn="score_design_centroid" blueprint="%%blueprint%%" />
		<BluePrintBDR name="build_mainchain" scorefxn="score_design_centroid" use_abego_bias="True" blueprint="%%blueprint%%" />

		<ParsedProtocol name="mainchain_building_protocol">>
			<Add mover="build_mainchain"/>
			<Add mover="dssp"/>
		</ParsedProtocol>

		<LoopOver name="mainchain_building_loop" mover_name="mainchain_building_protocol" filter_name="compound_toplogy_filter" iterations="9999" drift="False" ms_whenfail="FAIL_DO_NOT_RETRY" />

		<!-- search for disulfide bond positions -->
		<Disulfidize name="disulfidizer" min_disulfides="2" max_disulfides="3" match_rt_limit="1" score_or_matchrt="true" max_disulf_score="0" min_loop="5" use_l_cys="true" keep_current_disulfides="false" include_current_disulfides="false" use_d_cys="false" />

		<!-- perform design on each combination of disulfide bond patterns with the multiple pose mover -->
		<MultiplePoseMover name="MPM_design" max_input_poses="20">
			<SELECT>
				<TopNByProperty n="20" order="descending">
					<FilterReporter filter="disulfide_entropy"/>
				</TopNByProperty>
			</SELECT>
			<ROSETTASCRIPTS>
			
			
				<SCOREFXNS>
			
					<!-- the current default score function with the coordinate constraint energy term enabled -->
					<ScoreFunction name="score_design" weights="ref2015">
						<Reweight scoretype="aa_composition" weight="1"/>
						<Reweight scoretype="buried_unsatisfied_penalty" weight="1.0" />
					</ScoreFunction>
			
					<!-- the current default energy function without additional energy terms -->
					<ScoreFunction name="score_evaluate" weights="ref2015"/>
			
				</SCOREFXNS>
			
			
				<TASKOPERATIONS>
			
					<!-- standard task operations used for design -->
					<LimitAromaChi2 name="limitchi2" include_trp="1" />
					<ExtraRotamersGeneric name="extra_rotamers" ex1="True" ex2aro="True" />
					<IncludeCurrent name="include_starting_rotamers" />
					<ConsensusLoopDesign name="disallow_nonnative_loop_sequences" />
			
					<!-- layer design for flexible backbone design -->
					<LayerDesign name="layer_all" layer="core_boundary_surface" verbose="False" use_sidechain_neighbors="True"/>
			
					<!-- task operations for filters -->
					<LayerDesign name="layer_core_boundary" layer="core_boundary" verbose="False" use_sidechain_neighbors="True" />
					<OperateOnCertainResidues name="no_repack_non-disulf">
						<ResidueName3Isnt name3="CYS" />
						<PreventRepackingRLT/>
					</OperateOnCertainResidues>

				</TASKOPERATIONS>
			

				<FILTERS>
			
					<SheetTopology name="filter_strand_pairing" topology="%%topology%%" blueprint="%%blueprint%%" confidence="0" />
					<SecondaryStructureCount name="count_SS_elements" filter_helix_sheet="True" num_helix="1" num_sheet="3" num_helix_sheet="4" min_helix_length="5" min_sheet_length="3" min_loop_length="2" confidence="1" /> 
					<TaskAwareScoreType name="dslf_quality_check" task_operations="no_repack_non-disulf" scorefxn="score_evaluate" score_type="dslf_fa13"  mode="individual" threshold="-0.5" confidence="1" />
					<SecondaryStructureHasResidue name="ss_contributes_core" secstruct_fraction_threshold="1.0" res_check_task_operations="layer_core_boundary" required_restypes="VILMFYW" nres_required_per_secstruct="1" filter_helix="1" filter_sheet="1" filter_loop="0" min_helix_length="4" min_sheet_length="3" min_loop_length="1" confidence="1" />
			
				</FILTERS>
			
			
				<MOVERS>
			
					<!-- assign secondary structure information to the pose -->
					<Dssp name="dssp" />
			
					<!-- for adding and removing helix sequence design constraints -->
					<AddHelixSequenceConstraints name="apply_helix_sequence_constraints" />
					<ClearCompositionConstraintsMover name="remove_sequence_constraints" />
			
					<!-- flexible backbone design -->
					<FastDesign name="fastdesign" relaxscript="rosettacon2018" task_operations="extra_rotamers,limitchi2,disallow_nonnative_loop_sequences,layer_all" scorefxn="score_design" repeats="3"/>
			
					<!-- relax without design specific energy terms prior to filtering and scoring -->
					<FastRelax name="fastrelax" scorefxn="score_evaluate" repeats="1" task_operations="limitchi2,extra_rotamers,include_starting_rotamers"/>
			
				</MOVERS>
			
			
				<PROTOCOLS>
			
					<Add mover_name="dssp" />
					<Add mover_name="fastdesign" />
					<Add mover_name="fastrelax" />
					<Add filter_name="filter_strand_pairing" />
					<Add filter_name="count_SS_elements" />
					<Add filter_name="dslf_quality_check" />
					<Add filter_name="ss_contributes_core" />
			
				</PROTOCOLS>
			
			
			</ROSETTASCRIPTS>

		</MultiplePoseMover>

	</MOVERS>


	<PROTOCOLS>

		<Add mover="dssp"/>
		<Add mover_name="assign_secondary_structure_bonus"/>
		<Add mover_name="mainchain_building_loop" />
		<Add mover_name="disulfidizer" />
		<Add mover_name="MPM_design" />

	</PROTOCOLS>


</ROSETTASCRIPTS>

EHEE.blueprint

SSPAIR 1-3.A.0;2-3.A.0
HSSTRIPLET 1,3-1
1 V LE .
2 V EB R
0 V EB R
0 V EB R
0 V EB R
0 V EB R
0 V EB R
0 V EB R
0 V LG R
0 V LB R
0 V LB R
0 V HA R
0 V HA R
0 V HA R
0 V HA R
0 V HA R
0 V HA R
0 V HA R
0 V HA R
0 V HA R
0 V HA R
0 V HA R
0 V HA R
0 V HA R
0 V HA R
0 V HA R
0 V LG R
0 V LB R
0 V EB R
0 V EB R
0 V EB R
0 V EB R
0 V EB R
0 V EB R
0 V EB R
0 V LE R
0 V LA R
0 V EB R
0 V EB R
0 V EB R
0 V EB R
0 V EB R
0 V EB R
0 V EB R
0 V LO R

example_EHEE.pdb

ATOM      1  N   GLY A   1      88.626  45.321  53.239  1.00  0.00           N  
ATOM      2  CA  GLY A   1      88.882  45.117  51.821  1.00  0.00           C  
ATOM      3  C   GLY A   1      87.985  46.008  50.978  1.00  0.00           C  
ATOM      4  O   GLY A   1      87.641  45.666  49.847  1.00  0.00           O  
ATOM      5  HA  GLY A   1      89.922  45.371  51.617  1.00  0.00           H  
ATOM      6  N   GLY A   2      87.607  47.154  51.534  1.00  0.00           N  
ATOM      7  CA  GLY A   2      86.810  48.133  50.805  1.00  0.00           C  
ATOM      8  C   GLY A   2      87.107  49.550  51.281  1.00  0.00           C  
ATOM      9  O   GLY A   2      87.542  49.755  52.414  1.00  0.00           O  
ATOM     10  HA  GLY A   2      87.060  48.063  49.746  1.00  0.00           H  

run_EHEE.sh

#!/bin/bash
dsub \
	--provider local \
	--logging gs://ipi-main/chris_bahl/rosetta_docker_demo/runlogs \
	--tasks gs://ipi-main/chris_bahl/rosetta_docker_demo/tasks.tsv \
	--input SCRIPT=gs://ipi-main/chris_bahl/rosetta_docker_demo/build_and_disulfidize.xml \
	--input BLUEPRINT=gs://ipi-main/chris_bahl/rosetta_docker_demo/EHEE.blueprint \
	--input PDB=gs://ipi-main/chris_bahl/rosetta_docker_demo/example_EHEE.pdb \
	--output-recursive OUTPUT=gs://ipi-main/chris_bahl/rosetta_docker_demo/output \
	--image gcr.io/ipi-main/rosetta-main:2018.33_HEAD.7111c54 \
	--command 'rosetta_scripts \
		-in:file:s ${PDB} \
		-parser:protocol ${SCRIPT} \
		-out:path:all ${OUTPUT} \
		-out:suffix ${SUFFIX} \
		-parser:script_vars \
			blueprint=${BLUEPRINT} \
			topology=1-3.A.0;2-3.A.0 \
		-nstruct 5 \'