You are here

Repeating sequence in Rosetta de novo protein folding

3 posts / 0 new
Last post
Repeating sequence in Rosetta de novo protein folding


I am trying to do a de novo protein folding from a protein sequence with repeating Gly and Arg only.

So the sequence looks like GRGRGRGRGR..... I put the sequence onto Robetta Fragment Server and it gave me this error message:


Target:    GR25
Status:    Error
Date Submitted:    02/07/18 01:54:32 AM
Started:    02/07/18 04:29:00 AM
Ended:    02/07/18 05:07:22 AM
Expires:    02/14/18 05:07:22 AM   (6 days 08:41:40)
Length:    50
Exclude Homologues:    no

sam target99 failed! 


This might be a dumb question but I was wondering if there are some restrictions on the usage of de novo protein folding in Rosetta when the sequence is repeating...?

Thanks for your help! 




Post Situation: 
Wed, 2018-02-07 20:52

Fragment prediction is based on finding chunks of PDBs with similar sequences and/or similar predicted secondary structure to the request.  I would guess that nothing looks like this that's in the PDB, so the system errors out.  I guess try BLASTing this sequence against what's been crystallized to see if there are any hits.

Thu, 2018-02-08 09:16

Do you have any reason to believe that your sequence will be folded/structured in vivo?

If you perform disorder prediction by submitting that sequence to DISOPRED3 at then you will see that it is predicted to be "disordered state, protein binding"  with a confidence near 1.0.

Warning: If you ask Rosetta to fold a sequence, it will give you the best folded structure it can find. But if that sequence prefers to be unstructured, then your prediction may have little value.


Thu, 2018-02-08 21:18