Enabling N-Linked Glycans

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    • June 5, 2014 at 6:51 pm #1907
      Anonymous

        Hello,

        I am currently trying to analyze a crystal structure that has various N-linked Glycans attached and would like to be able to work with these glycans in PyRosetta. However, if I try to work with the structure without cleaning it I receive the error message:

        >>>pose = pose_from_pdb(“my_molecule.pdb”)
        core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 9172 residue types

        ERROR: unrecognized aa NAG
        ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 1424
        Traceback (most recent call last):
        File ““, line 1, in
        RuntimeError: unidentifiable C++ exception

        Is there currently defined residue types that I can add to my pyrosetta library that define these glycans or ways to work with uncleaned pdb files?

        Any help or suggestions would be greatly appreciated.

        Thanks,

        Justin

      • June 6, 2014 at 2:57 pm #10084
        Anonymous

          Hello, Justin,

          I am actually actively developing the means to add such functionality into Rosetta, but it is a work in progress. If you have a recent Linux or Mac version of PyRosetta, much of it has already been added, but the features are incomplete, untested, and unpublished.

          There are 3 flags you would need to use to enable the functionality. Within PyRosetta (again, only the Linux and Mac versions), you would use rosetta.init(“-include_sugars -read_pdb_link_records -enable_branching”).

          You also need to change the PDB file so that the string “NAG” is changed to “Glc”. (Rosetta will figure out that it is a modified GlcNAc automatically.)

          You also need to maintain the LINK records in the PDB file.

          You also need to change a few atom names in the PDB file for the GlcNAc records to match those used by Rosetta (as can be seen in the Rosetta database in the patch file for N-acetylated sugars).

          It is not entirely straightforward yet, because bugs are being worked out and various helper scripts are still being written. It is probably best if you e-mail me directly, and I can collaborate with you in getting what you want to work to work.

          ~Labonte

        • September 27, 2014 at 2:02 pm #10341
          Anonymous

            Hello,

            I am also extremely interested in the study of N-glycoproteins. I wonder if there has been any updates since the last comment. Also, is there a way to make it work on PyRosetta on Windows?

            Thanks,

            Tony

          • October 6, 2014 at 9:56 pm #10389
            Anonymous

              Hello, Tony,

              Yes, I am fairly certain that the newest Windows PyRosetta release should now include the carbohydrate functionality I mentioned above.

              I will restate again, however, that it is a work-in-progress, incomplete, untested, and unpublished. Feel free to e-mail me directly if you have any questions.

              ~Labonte

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