How to estimate the effect of a mutation on the binding energy?

Member Site Forums Rosetta 3 Rosetta 3 – Applications How to estimate the effect of a mutation on the binding energy?

  • This topic has 4 replies, 3 voices, and was last updated 13 years ago by Anonymous.
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    • #788
      Anonymous

        Given a protein complex, I would like to estimate the effect of a point mutation on the binding energy (ddG). I’d appreciate if anyone could point me to the Rosetta app(s) that I should look into. I’m fairly new to Rosetta.

        Thanks!

      • #5030
        Anonymous

          I’ve asked around to see if there’s a DDG app already present in 3.2.

          If not, doing it with fixbb is pretty simple:
          1)Get PDBs of the bound complex and each monomer.
          2)Calculate dG of binding by packing them separately subtracting their scores AB-A-B.
          3)Do 2) again with the mutation in place (via resfile)
          4) subtract 3 from 2 and you have ddG.

        • #5040
          Anonymous

            After consultation, it seems there isn’t a released executeable for this; your best bet is the steps I described.

          • #5239
            Anonymous

              If that doesn’t work for you, there is a script written by Sid Chaudhury to do just that in PyRosetta:
              http://www.pyrosetta.org/scripts

            • #5041
              Anonymous

                Thank you very much for looking into this! I’m giving your suggestion a try.

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