[Solved] Docking to a trimer

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    • #443

        I’m trying to dock a peptide (35 aa) to a trimeric receptor (P2X4, pdb: 3I5D). I need that these three subunits behaved as a single unit, without a jump, and peptide was docked to this assembly.

        But I probably misunderstand how to setup a docking fold tree: constructs like dock_prot.setup_foldtree(p, “T_ABC”) or dock_prot.setup_foldtree(p, “ABC_T”) don’t work since I have monomers (A, B, C) moving as well as the peptide (T).
        The fold tree looks as following:

        FOLD_TREE EDGE 1 324 -1 EDGE 324 325 1 EDGE 325 332 -1 EDGE 332 333 2 EDGE 333 660 -1 EDGE 660 661 3 EDGE 661 985 -1 EDGE 985 986 4 EDGE 986 1012 -1

        What do I have to do to have this done & start docking with all three (A, B, C) subunits not moving?

      • #4354

          Actually, solution was simple: I did not use DockingProtocol() at all, instead of it I made fold tree manually, the first edge of which covered all three subunits:

          ft = FoldTree()





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