I am not sure if this is the best way but I always use Blastp and search against PDB. Dali search would be more appropriate if you have a structure of your protein.
Zhen From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Gloria Borgstahl Sent: Thursday, August 22, 2013 11:15 AM To: [email protected] 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
