How to model a protein that dimerizes to a small molecule?

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    • May 25, 2011 at 2:29 pm #921
      Anonymous

        I have a protein that dimerizes to a GAG molecule, and I would like to model the dimerization to the GAG using Rosetta. I have attempted to use Rosetta Docks to calculate the interaction; however, the GAG molecule is removed from the PDB files. First question is should I be using RosettaLigand, and if so is RosettaLigand able to model ligand binding to two protein molecules? Would it be best to take the model from RosettaDock for a RosettaLigand run with the GAG compound? Thank you for your assistance.
        Cheers,

        Paul Holland, Ph.D

      • May 25, 2011 at 7:55 pm #5644
        Anonymous

          Did you mean to post this in the ++ forum, or the Rosetta 3 forum? I’m assuming the latter. If the former, ++ is no longer under development; you’ll probably have to try iterating between the two modes (and will have trouble getting help).

          Rosetta3 in general can address the problem of two proteins and one ligand, but I don’t know that there is a prewritten tool for it. You may need to generate your own using RosettaScripts. I’ve forwarded the question to the docking and ligand guys for comment.

        • May 26, 2011 at 1:10 am #5657
          Anonymous

            Thank you I will try that. I meant to post to Rosetta 3. I must have clicked on the wrong tab for the post.

          • May 25, 2011 at 8:46 pm #5653
            Anonymous

              The docking and ligand guys agree that you’ll want to write your own protocol in RosettaScripts that iterates between ligand docking and protein docking as you see fit.

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