<!--- This XML script represents the Transform/MCM protocol described in the manuscript. See manuscript for detailed explanation of protocol -->
<ROSETTASCRIPTS>
<SCOREFXNS>
<!--- ligand_soft_rep is used during the HighResDocker stage of refinement -->
<ScoreFunction name="ligand_soft_rep" weights="ligand_soft_rep">
<Reweight scoretype="fa_elec" weight="0.42"/>
<Reweight scoretype="hbond_bb_sc" weight="1.3"/>
<Reweight scoretype="hbond_sc" weight="1.3"/>
<Reweight scoretype="rama" weight="0.2"/>
</ScoreFunction>
<!--- ligand_soft_rep is used during the FinalMinimizer stage of refinement and scoring -->
<ScoreFunction name="hard_rep" weights="ligand">
<Reweight scoretype="fa_intra_rep" weight="0.004"/>
<Reweight scoretype="fa_elec" weight="0.42"/>
<Reweight scoretype="hbond_bb_sc" weight="1.3"/>
<Reweight scoretype="hbond_sc" weight="1.3"/>
<Reweight scoretype="rama" weight="0.2"/>
</ScoreFunction>
</SCOREFXNS>
<!--- ligand areas, interface builders and movemap builders are used to define the interface region between the protein and the ligand -->
<LIGAND_AREAS>
<LigandArea name="docking_sidechain" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<LigandArea name="final_sidechain" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<LigandArea name="final_backbone" chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
</LIGAND_AREAS>
<INTERFACE_BUILDERS>
<InterfaceBuilder name="side_chain_for_docking" ligand_areas="docking_sidechain"/>
<InterfaceBuilder name="side_chain_for_final" ligand_areas="final_sidechain"/>
<InterfaceBuilder name="backbone" ligand_areas="final_backbone" extension_window="3"/>
</INTERFACE_BUILDERS>
<MOVEMAP_BUILDERS>
<MoveMapBuilder name="docking" sc_interface="side_chain_for_docking" minimize_water="true"/>
<MoveMapBuilder name="final" sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
</MOVEMAP_BUILDERS>
<!--- if you use the Transform mover, you must specify 1 or more scoring grids. In this case, ClassicGrid is identical to the grid used by the Translate and Rotate movers-->
<SCORINGGRIDS ligand_chain="X" width="30">
<ClassicGrid grid_name="vdw" weight="1.0"/>
</SCORINGGRIDS>
<MOVERS>
<!--- in the Transform mover, initial_perturb="5.0" means that hte ligand will initially be translated by up to 5.0 Angstroms to avoid bias in benchmarking -->
<Transform name="transform" chain="X" box_size="20.0" move_distance="0.1" angle="5" cycles="500" repeats="1" temperature="5" initial_perturb="5.0"/>
<!--- as configured here, HighResDocker will perform a single round of repacking -->
<HighResDocker name="high_res_docker" cycles="1" repack_every_Nth="1" scorefxn="ligand_soft_rep" movemap_builder="docking"/>
<FinalMinimizer name="final" scorefxn="hard_rep" movemap_builder="final"/>
<InterfaceScoreCalculator name="add_scores" chains="X" scorefxn="hard_rep" compute_grid_scores="0"/>
</MOVERS>
<PROTOCOLS>
<Add mover_name="transform"/>
<Add mover_name="high_res_docker"/>
<Add mover_name="final"/>
<Add mover_name="add_scores"/>
</PROTOCOLS>
</ROSETTASCRIPTS>