Snugdock versus Docking with an ensemble of protein conformations

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    • March 29, 2019 at 5:07 pm #3101
      Anonymous

        Is Snugdock essentially the same as running Docking with an ensemble of conformations generated by Relax?

      • March 29, 2019 at 5:34 pm #14625
        Anonymous

          Hi Mike,

          Not quite. SnugDock is specific to antibody–antigen complexes and builds on the docking protocol to include CDR H2/H3 loop refinement steps. Comparing SnugDock to docking with ensembles, the H2/H3 motions will be larger than those in a relaxed ensemble, while there would be no motion elsewhere. The best approach is to run SnugDock with ensembles, if you are docking an antibody-antigen complex.

          Best,

          Jeliazko

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