is it possible to model a antibody (or just the cdr3 loop) in the presense of an antigen structure (already docked to it)?
thakns for the help!
I would recommend the SnugDock algorithm for this sort of project. If you are already confident in your overall orientation then you can choose to use only the high-resolution portion of the method.
It looks just like what I was looking for.
Thanks for the quick reply!
How can I choose only the high-resolution portion?
I can't find any flag for this... (there is a flag -low_res_protocol_only but not -high_res_protocol).
My understanding of the docs and code is that the flag '-low_res_protocol_only' applies to the global docking search. There is also the '-docking_local_refine' flag, and you would want to set these to 'false' and 'true', respectively. There may still be a low-res stage for the CDR-H3 remodeling.
You might also find this Gray lab pre-print useful as well, in case you have not seen it: https://www.biorxiv.org/content/10.1101/2020.05.26.116210v1