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.
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.