a question about ligand docking

Member Site Forums Rosetta 3 Rosetta 3 – Applications a question about ligand docking

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    • #1290

        Hi,I am a brand new user in using Rosetta.
        In my case, I want to dock a ligand to a protein with the protein conformation fixed.
        I have tried default protocol of ligand_docking but it did not work.
        The conformation of some side chains changed.
        So, does someone have the idea of designing a proper protocol to achieve this goal?
        Thanks in advance.

      • #7163

          Try adding the flag -packing:prevent_repacking and see if that works.

        • #7175

            Thank smlewis.
            But this option did not work.
            Side chains still changed their rotamers.

          • #7176

              What sorts of side chains are changing? Is it only certain residue types, particularly only polars? Is it residues that are complete in the pdb or is it residues that are partially missing in the pdb?

            • #7177

                I think I should also ask why do you want your side chains not to change it all?

              • #7178

                  My purpose is verifying the mechanism of docking an oligosaccharide molecule to a hexosaminidase.
                  Actually this mechanism has already been confirmed by the complex structures solved by X-ray crystallography.
                  In this mechanism, the side chain conformations of some critical interface residues should not be changed.
                  However, in the docking results, the conformations of these residues changed.
                  So, I hope that there is a protocol through which the ligand can be docked to the protein with the conformation of side chain fixed.
                  In this way, I think that the docking score may make more sense.

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