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Fragments for short peptides using Robetta

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Fragments for short peptides using Robetta

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

Post Situation: 
Wed, 2018-05-16 14:21

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?

Wed, 2018-05-16 15:07

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?

Fri, 2018-05-18 13:44

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.


Mon, 2018-06-04 00:04