Hi Gloria,
I've gotten useful results from these two threading / prediction servers:
Raptorx and Phyre (for low homology, I found the original version works better
than phyre2).
Phoebe
++++++++++++++++++++++++++++++++++++++++++
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
773 834 1723; [email protected]
http://bmb.bsd.uchicago.edu/Faculty_and_Research/
http://www.rsc.org/shop/books/2008/9780854042722.asp
________________________________________
From: CCP4 bulletin board [[email protected]] on behalf of
[email protected] [[email protected]]
Sent: Thursday, August 22, 2013 11:36 AM
To: [email protected]
Subject: Re: [ccp4bb] structural search for homologs in pdb?
Dear Gloria,
If you are searching with a protein sequence, you could also try FFAS
(ffas.burnham.org/). This will perform profile-profile alignments to do fold
recognition. Works quite well for low homology cases in particular.
HTH and best wishes,
Mohammad
