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Rosetta antibody- modeling in the presense of an antigen

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Rosetta antibody- modeling in the presense of an antigen


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!


Post Situation: 
Mon, 2021-02-01 03:19

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.

Good luck!

Mon, 2021-02-01 08:26

It looks just like what I was looking for.

Thanks for the quick reply!

Tue, 2021-02-02 05:26

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).

Thanks again

Wed, 2021-02-03 03:29

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: 

Wed, 2021-02-03 08:52