I'm trying to model a structure of an antibody. I have an initial starting structure, which I have generated using a separate online server, and I have prepared the structure for modeling with rosetta. I've been using the application "antibody_model_CDR_H3" which simultaneously docks Vh-Vl and samples loop conformations for HCDR3.
Is there a recommended way to also allow rosetta to resample loop conformations for the other CDR loops? Ideally I'd like to sample relevant loops from the Dunbrack CDR cluster database. The rosetta documentation hints that this is possible in pyrosetta or through movers. Can anyone provide information on how I can accomplish this?
Some of this is possible, but currently it can be fairly tricky. There are some work arounds I can describe. We are currently finishing up the Rosetta antibody design program and the thought is that it should be possible to use the same machinery for modeling in the way you describe. Are you a Rosetta developer? If so, I might be able to get the modeling component of the design code done sooner rather than later. Otherwise, perhaps we can talk offline? My email is firstname.lastname@example.org