add water into protein interfaces using solvated rotamer?

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    • July 20, 2013 at 2:33 pm #1667
      Anonymous

        Hello,

        Im new to Rosetta. Im trying the tutorials of PyRosetta, but I couldn’t find any clues that could help me add water into the protein interfaces using the Solvated Rotamers (as stated in the paper by Jiang et al. 2005 “A solvated rotamer” approach to modeling water-mediated hydrogen bonds at protein-protein interfaces).

        Anyone please suggests me any hint or readings that I can find how to do it!

        Thank you very much.

        Regards,
        Chinsu

      • July 22, 2013 at 5:54 pm #9098
        Anonymous

          The solvated rotamer work was done in Rosetta++ (2.X), and the code to do it doesn’t appear to have been transferred to Rosetta 3.X or PyRosetta. My understanding is that the approach did not turn out to be as useful as was originally hoped, so work on it stalled, and no one bothered to extend the effort to transition the algorithm from the Rosetta 2 codebase to the Rosetta 3 codebase.

          That said, I may have missed it, and someone could be along to point out what dusty corner it’s hiding in.

        • July 22, 2013 at 7:39 pm #9100
          Anonymous

            Rocco, I found the option explicit_h2o in the options system, with the description “Use rotamers with explicit waters”. However, searching for the code that uses it doesn’t turn up much of anything either….

          • July 25, 2013 at 4:24 am #9122
            Anonymous

              Oh, thanks for this explicit_h2o, but I couldnt find it though. I’ve tried to search for it in the manual, but the closest hit came out as the “packing” which is somehow related to the rotamers. Not much either.
              I may dig it in the ROsetta 2, but Im more comfortable with Python though.

              Thank you.

              Chinh

            • July 25, 2013 at 4:47 pm #9126
              Anonymous

                chinhusutran,

                The option is in the rosetta source file source/src/basic/options/options_rosetta.py This file houses ALL of the rosetta options, and is a great place to start. These options can be set in (newest) PyRosetta by doing:
                my_options = [“-option1”, “-option2”]
                rosetta.init(” “.join(my_options))

                There is some water rotamer code it looks like in Rosetta source, but I am unsure how much it works, how exactly to use it, or if it even works (As Rocco said, some things were lost in translation between Rosetta2 and 3. You could download Rosetta 3.5 source to check the existing code out. Unfortunately, I’m not sure how much of it will work in PyRosetta.

                The code is in source/src/core/pack/rotamer_set/rotamer_building_functions.cc with the .hh having minimal documentation of the functions.
                The code that brought me there is source/src/core/pack/rotamer_set/RotamerSet_.cc + .hh (search for water)

                If you don’t want to go down this rabbit hole, you could download and try Rosetta2 as an alternative.

                -J

              • July 26, 2013 at 5:19 am #9134
                Anonymous

                  jadolfbr,

                  Thanks a lot.

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