I am interested in docking a camelid VHH to antigen. As far as I can tell SnugDock requires both the heavy and light chains. (I know there will be some problems with my H3 loop.)
Does anyone know a work-around for this?
Snugdock is extremely specialized; I don't think it can do this. My best guess is that you'd want to duplicate the snugdock idea by cobbling together docking and loop remodeling movers in RosettaScripts. I'll see if the antibody people have any better ideas.
One strength of SnugDock is it's re-docking of the VH-VL relative orientation during antibody-antigen docking. Unfortunately, this is also a weakness as it requires the assumption of a VL chain. I agree, the best work around is a RosettaScript with alternating antibody-antigen docking and re-modeling of the CDR loops. I'd be glad to help with this.
I am new to Rosetta. My zero task is to start by learning how to do the docking by working off of a solved structure. Once I understand how to do a local dock without needing to remodel the loops, I will follow up.
I think I made SnugDock work with Camelid antibodies some time ago. Basically, it would skip the Vl/Vh optimization step. Please try it out and post any error messages here and we should be able to get it to work.
More comments from the antibody crew:
"SnugDock doesn't make sense for camelids -- VH-VL rigid body stuff not needed. I'd suggest using EnsembleDock with a set of different H3 loop conformations." -- Jeff Gray
Same situation as David Weis, trying to dock VHH to antigen. Successful at docking pdb 5B8C (VL-VH to Cell death protein PD1) but failed when trying to dock VH alone to PD1. Attached is the log file and the pdb input.
Any help would be greatly appreciated. Thanks.
As was mentioned, the SnugDock protocol is specifically intended to sample the internal degrees of freedom between the heavy and light chains during antibody/antigen docking. It doesn't really make sense to use SnugDock to dock a single chain (e.g. no light chain) antibody. Use a regular docking protocol instead.