Rosetta antibody- modeling in the presense of an antigen

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    • February 1, 2021 at 11:19 am #3680
      Anonymous

        Hi,

        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!

         

      • February 1, 2021 at 4:26 pm #15700
        Anonymous

          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!

          • February 2, 2021 at 1:26 pm #15701
            Anonymous

              It looks just like what I was looking for.

              Thanks for the quick reply!

            • February 3, 2021 at 11:29 am #15702
              Anonymous

                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

              • February 3, 2021 at 4:52 pm #15703
                Anonymous

                  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 

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