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:
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)
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!
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.
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 bioinf.cs.ucl.ac.uk/psipred/ 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.