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