constraints in Rosetta ligand docking (AddorRemoveMatchCsts, Addconstraints Mover, and ConstraintSetMover)

[Anonymous]

Hello,

I am performing Rosetta ligand docking for an enzyme A to a ligand X which should be covalently bound to a small protein B.  I need to impose this covalent bond and some other catalytic constraints (distances between ligand and receptor’s residues and also the distances between two residues of the receptors )  to my ligand docking.  I  found several movers for adding constraints including AddorRemoveMatchCsts, Addconstraints Mover, and ConstraintSetMover, but I am confused about which one works with Rosetta Ligand docking. 

I have studied Rosetta documentation and I saw “AddorRemoveMatchCsts” is used in EnzymeDesign protocol. I was thinking to add “AddorRemoveMatchCsts” to ligand docking movers since it allows me to define the covalent bond. In other words, the protocols would be like below.

 

Moreover, I was wondering whether I need to generate more 100 conformers for my ligand since it is large (it has 25 rotatable bonds).

 

I really appreciate it if you could help me in this regard.

      <MOVERS>

              <AddOrRemoveMatchCsts name=”cstadd” cst_instruction=”add_new”/>

                        <Transform name=”transform” chain=”X” box_size=”10.0″ move_distance=”0.25″ angle=”20″ cycles=”500″ repeats=”1″ temperature=”5″  initial_perturb=”5″/>

                        <HighResDocker name=”high_res_docker” cycles=”6″ repack_every_Nth=”3″ 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”/>

                        <ConstraintSetMover name=”refinement_constraint” add_constraints=”True” cst_file=”../input_files/refinement_constraint.cst”/>

                        <StartFrom name=”mystart” chain=”X” use_nbr=”true” >

                                <Coordinates x=”20.037″ y=”35.45″ z=”74.245″/>

                        </StartFrom>

                </MOVERS

                <PROTOCOLS>

                         <Add mover_name=”cstadd”/>

                        <Add mover_name=”mystart”/>

                        <Add mover_name=”transform”/>

                        Add mover=”refinement_constraint” />

                        <Add mover_name=”high_res_docker”/>

                        <Add mover_name=”final”/>

                        <Add filter=”ACP_connection”/>

                        <Add filter=”D281″/>

                        <Add filter=”E319″/>

                        <Add filter=”hb_D281_H285″/>

                        <Add filter=”hb_D281_N283″/>

                        <Add mover_name=”add_scores”/>

                </PROTOCOLS>

[Author]

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