Noncanonical amino acids

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    • March 18, 2014 at 12:29 pm #1853
      Anonymous

        Hi all,

        I am trying to implement the method outlined in “Incorporation of Noncanonical Amino Acids into Rosetta and use in Computational Protein- Peptide Interface Design” doi:10.1371/journal.pone.0032637.

        I just wondered if I should start right from the beginning, or whether there is somewhere I can download the parameter files, rotamer libraries and unfolded state reference energies for NCAAs so that I can move directly to doing the design protocol.

        Any advice would be most appreciated.

        wsgosal

      • March 21, 2014 at 3:50 pm #9914
        Anonymous

          Hi Walraj, I think we met at RosettaCon. Thanks for your interest in the NCAA paper. The ResidueType parameter files are distributed with Rosetta but are not enabled/turned-on by default. The rotamer libraries are not however are not distributed with Rosetta. You can download them at the link below.

          http://carl.bio.nyu.edu/~renfrew/ncaa/ncaa_rotamer_libraries.tar.gz

          Here is a quick reference for the three letter codes for the NCAAs

          http://fry2.bio.nyu.edu/~kdrew/rosetta/ncaa_codes

          I suspect that you will also find the protocol capture associated with this paper rather useful. You can find it in the demos directory of your copy of Rosetta.

        • March 25, 2014 at 9:32 am #9919
          Anonymous

            Hi Doug,

            Yes we did and thanks so much for this – really appreciate the help. Will let you know how I get on.

            Best,

            W.

          • April 10, 2016 at 7:58 pm #11507
            Anonymous

              The carl.bio.nyu.edu link appears to be broken now – are these still available somewhere?

            • April 29, 2016 at 2:49 pm #11549
              Anonymous

                Try the following DropBox links from Doug Renfrew:

                https://www.dropbox.com/s/a3g0caisrlan09j/ncaa_rotamer_libraries.tar.gz?dl=0

                https://www.dropbox.com/s/fqd7ywy1wzk6ujm/beta_amino_acid.tar.gz?dl=0

                https://www.dropbox.com/s/98l2lpshncdlqur/peptoid_rotlibs_kmc.tar.gz?dl=0

              • June 30, 2020 at 3:43 pm #15362
                Anonymous

                  Thanks for these!

                  By any chance do you have a key for the three letter codes used for the NCAAs?

                  The previously posted link seems to have also died.

                  Thanks!

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