short peptide fragment file generation

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    • July 11, 2016 at 7:04 am #2467
      Anonymous

        Hi Rosetta users,

        I was trying to generate fragment files for a short peptide (9-AA) for use in abinito FlexPepDock. I checked out the demo, but found it quite difficult to follow using make_fragments.pl. I learned from the forum that the perl script is a bit outdated and we should use either the Robetta server or the new fragment picker application.  However, Robetta doesn’t seem to accept very short sequences. Could anyone advise me how to use the new fragment picker application to generate fragments for short peptides. Thanks in advance!

      • July 11, 2016 at 12:44 pm #11720
        Anonymous

          The fragment picker application will require the secondary structure  (PSIPRED & other protocols. For short peptides only use PISPRED) and sequence profile (BLAST) information. These files can be created by running the make_fragments.pl script. Download the necessary executables and databases as required and change the paths in the make_fragments.pl file.

          Once those file are created you can use fragment_picker.{ext} executable to generate fragment file. See the demos for fragment picking.

          best!

        • July 11, 2016 at 2:07 pm #11721
          Anonymous

            What does “short peptides” mean?  You mean you’re having trouble getting fragments at all, or getting 9-mers for a 9-mer peptide, or getting 3-mers for an X-mer peptide?  Did you try Robetta yet?  It’s infinitely easier than installing all the secondary structure prediction tools that aren’t actually part of Rosetta (that’s why making fragments is hard: setting up the external dependencies and paths).

          • July 12, 2016 at 6:34 am #11722
            Anonymous

              I didn’t get any fragments yet, because I found setting up things for make_fragment.pl a bit difficult. Running the fragment_picker.linuxgccrelease itself is quite straightforward though. My peptide is a 9-mer, so I will need to generate 3-, 5-, 9-mer fragments for FlexPepDock. I tried Robetta but it requires sequence length to be 27-1000 aa. To make Robetta work for a 9-aa peptide, can we simply append a few random residues to my sequence and then remove their information in the resulting secondary structure prediction files? Then feed these files to fragment_picker to generate all fragments?

            • July 12, 2016 at 1:13 pm #11725
              Anonymous

                “To make Robetta work for a 9-aa peptide, can we simply append a few random residues to my sequence and then remove their information in the resulting secondary structure prediction files? Then feed these files to fragment_picker to generate all fragments?”

                Try it and find out!  I don’t know.

                All of the inputs to fragment picker are also individually available on the web as webservers, you can try going directly to those.

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