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Hi Gloria,
You can paste your protein sequence directly into the text search box of the RCSB PDB website (http://www.rcsb.org), and choose one of the sequence search autosuggestions.
You can also to try the PSI-BAST search to find more distantly related homologs: click on the Sequence option in the top search bar and then choose “options”.
On the advanced search page choose “PSI-BLAST” as the search tool.
Peter Rose
RCSB PDB
From: CCP4 bulletin board [mailto:[log in to unmask]]
On Behalf Of Gloria Borgstahl
Sent: Thursday, August 22, 2013 8:15 AM
To: [log in to unmask]
Subject: [ccp4bb] structural search for homologs in pdb?
We have a protein sequence that probably contains OB folds. What is the best way to search for the top structural homologs to this sequence in the pdb? G