Fragments for short peptides using Robetta

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    • May 16, 2018 at 9:21 pm #2923
      Anonymous

        Hi, is there a way to use Robetta for creating fragments for short peptides?

        Currently, there is a minimum length of 27 required.

        Cheers, René

      • May 16, 2018 at 10:07 pm #14236
        Anonymous

          Having not tried this – pad it to length with AAAAAAAAAAAA, and then edit the fragments file to the “right” length by deleting all frames that go past the “real” sequence?

        • May 18, 2018 at 8:44 pm #14244
          Anonymous

            Good idea, I’ll give it a try, thanks!

            But would it be possible to get rid of this restriction of 27AA on the server?

          • June 4, 2018 at 7:04 am #14251
            Anonymous

              After some analysis I would advise against the strategy of adding an polyAla tail. This changes the secondary structure prediction significantly!

              Please suggest to the ones maintaining the server to erase that length restriction.

              As it is possible to build fragments for short peptides locally, it should be possible to do on the server.

               

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