I apologize if this has been asked before, but I couldn't seem to find any information on it. Is the EnsembleDock protocol available in Rosetta3.5? I don't see a specific executable for it in the rosetta/source/bin directory. Do I just use -l <pdblist> instead of -s <pdbfile> in the normal docking protocol? And can I still use constraints in EnsembleDock?
I specifically want to do antibody-antigen docking, and I realize that SnugDock is available for this purpose (albeit in Rosetta 2.3.1 it seems, which I'll have to install). But I wasn't sure if you could still specify constraints in SnugDock as I have some constraint information that I would like to incorporate into the docking simulation. We potentially would know or have a good idea about what part of the antigen binds to the CDRs, so if that information cannot be incorporated into SnugDock I was thinking of using EnsembleDock instead. Can anybody advise on whether this is a good plan or not? Thank you in advance for your assistance!