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