Enzyme-Ligand Docking with a Fixed Cofactor - XML file

[GiliWolf]

Hi,

I'm new to Rosetta and trying to perform enzyme-ligand docking with an extra cofactor.

In my first attempt, Rosetta misplaced both the ligand and the cofactor. Since the enzyme and cofactor were crystallized together, I want to keep them fixed while allowing only the ligand to move during docking.

I’d appreciate help with adjusting my XML file or any suggestions for specific parameters I should look into. So far, I've only used the generic dock.xml file from the Rosetta ligand_docking tutorial.

Thanks!

those are my input files -
-in
-file
-s AKR1B1_DGal_NADP.pdb # concnated enzyme-ligand-cofactor structure
-extra_res_fa DGal.params # ligand params
-extra_res_fa NADP.params #cofactor params

and this is the XML -

    <SCOREFXNS>
        <ScoreFunction name="ligand_soft_rep" weights="ligand_soft_rep">
        </ScoreFunction>
        <ScoreFunction name="hard_rep" weights="ligand">
        </ScoreFunction>
    </SCOREFXNS>

    <LIGAND_AREAS>
        <LigandArea name="inhibitor_dock_sc" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="false"/>
        <LigandArea name="inhibitor_final_sc" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="false"/>
        <LigandArea name="inhibitor_final_bb" 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="inhibitor_dock_sc"/>
        <InterfaceBuilder name="side_chain_for_final" ligand_areas="inhibitor_final_sc"/>
        <InterfaceBuilder name="backbone" ligand_areas="inhibitor_final_bb" extension_window="3"/>
    </INTERFACE_BUILDERS>

    <MOVEMAP_BUILDERS>
        <MoveMapBuilder name="docking" sc_interface="side_chain_for_docking" minimize_water="false"/>
        <MoveMapBuilder name="final" sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="false"/>
    </MOVEMAP_BUILDERS>

    <SCORINGGRIDS ligand_chain="X" width="15">
        <ClassicGrid grid_name="classic" weight="1.0"/>
    </SCORINGGRIDS>

    <MOVERS>
        <Transform name="transform" chain="X" box_size="7.0" move_distance="0.2" angle="20" cycles="500" repeats="1" temperature="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"/> 
    </MOVERS>

    <PROTOCOLS>
        <Add mover_name="transform"/>
        <Add mover_name="high_res_docker"/>
        <Add mover_name="final"/>
        <Add mover_name="add_scores"/>
    </PROTOCOLS>

[roccomoretti]

From a quick scan, it looks like the XML is as it should be.

One thing to double check is the chain designations. Since the RosettaLigand protocol uses chain letters to determine which residue it's docking, if you have your cofactor labeled as chain X, then there's a good chance the protocol will move the cofactor instead of the ligand. Make sure the ligand and cofactor have separate chain letters, and make sure that the ligand's chain letter is X.

[GiliWolf]

Thank you so much! The chain wasn't the problem, but I solved it by removing the params file of the cofactor and changing the input file to an enzyme+cofactor as one complex.
Do you happen to know a parameter that helps control the docking to a specific binding site in the enzyme?
Thanks!

[roccomoretti]

The binding site of RosettaLigand is controlled by the input structure. You can either change your input PDB, or adjust this by using a mover before the Transform mover which explicitly changes the location of the ligand. The StartFromMover is a standard choice, and has several methods for specifying the location of where to place the ligand.

[Skyx2025]

Hey Gili, hey Rocco,

I am currently trying to solve a similar problem in Rosetta. I would like to “fix” the cofactor heme in CYP3A4 before I actually perform ligand docking with API.

As I am also new to bioinformatics and Rosetta, I wanted to ask how exactly you (@GiliWolf) changed the input file in enzyme + cofactor (= cofactor covalently bound to enzyme?) and whether it is even possible to use the path described first (input files: protein.pdb + heme.params (fixed) + ligand.params?). Did you test Rocco's tip about the side chain letter back then? :)

I am very grateful for any help. Thank you in advance!

[dgront]

Hello, I got this email by RosettaCommons/rosetta mailing list. I am responding to it because a few years ago my lab did very similar docking calculations. The protocol has been described here: https://labnotes.readthedocs.io/en/latest/doc/pyrosetta_p450_docking.html#pyrosetta-cyp51-docking The student who was working on that project has graduated a few years ago and part of the knowledge how it was done is already gone. However I am pretty sure I still have all the files required to repeat the calculations: flagfiles, rosetta scripts (XML) and heme.param Best regards, Dominik Gront niedz., 17 sie 2025 o 11:58 Skyx2025 ***@***.***> napisał(a):

…

Hey Gili, hey Rocco, I am currently trying to solve a similar problem in Rosetta. I would like to “fix” the cofactor heme in CYP3A4 before I actually perform ligand docking with API. As I am also new to bioinformatics and Rosetta, I wanted to ask how exactly you ***@***.*** <https://github.com/GiliWolf>) changed the input file in enzyme + cofactor (= cofactor covalently bound to enzyme?) and whether it is even possible to use the path described first (input files: protein.pdb + heme.params (fixed) + ligand.params?). Did you test Rocco's tip about the side chain letter back then? :) I am very grateful for any help. Thank you in advance! — Reply to this email directly, view it on GitHub <#339 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAC3MI6KM6SHEU7VEZKX5CL3OBG5RAVCNFSM6AAAAABXXSMINSVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMJTGEYTIMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.*** com>

[Skyx2025]

Hey Dominik,

thank you very much for your reply and for sharing your protocol - that's exactly what I was hoping/looking for!

Yesterday, I tried Rocco's first tip, which seems to have worked (heme = chain letter y) plus I added the StartFromMover command to the XML. Nevertheless, I'll take a closer look at your approach and make the necessary adjustments, since I still need to figure out which flags/scores are important for ligand docking ... :^)

Thanks again!!