does rosetta good at peptide-protein docking?

Member Site Forums Rosetta 3 Rosetta 3 – General does rosetta good at peptide-protein docking?

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    • #725

        Generally speak the peptide docking is much more chalenged than protein-protein docking for the peptide backbone is much more flexible than protein. Because of this reason, many peptide docking tools would introduce annealing and solvent model. I am wondering, does Rosetta also good at such kind of work?

        If I want to do a peptide docking, may I also use solvent model(such as TIP3 and so on) and annealing during the docking?


      • #4780

          FlexPepDock coming in 3.2 is the Rosetta program for peptide docking. It’s not quite out yet.

          Rosetta as a general rule does not use explicit solvent models. There are a few tools kicking around but mostly we use implicit solvent.

          What specifically do you mean by annealing? I assume FlexPepDock uses either a constant temperature or an annealing gradient during its Monte Carlo search but I do not know which.

        • #4782

            FlexPepDock has a free server, you can submit an initial peptide-protein complex and the peptide backbone should be in the protein binding site.

            • #4784

                SunH, thanks for pointing that out!

                Generally, the Rosetta servers (Design, Dock, Robetta (abinitio), FlexPepDock, others) do a great job for a first-pass model of a problem. A local installation of Rosetta running on a supercomputer/cluster will give better results than the servers will because a lot more computing muscle is available. (Actually, RosettaDesign can do complete treatments of most fixed-backbone problems provided the design space is sufficiently small – it’s a tired, wheezy old machine but the fixed-backbone problem is so well treated by Rosetta that even old hardware can handle it.)

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