Dear Marco, have you tried to perform the search for a template using fold recognition tools such as GenThreader, 3D-PSSM and so on? They use a different criterium to find a template with respect to BLAST and PSI-BLAST, and they are effective in finding templates when the similarity of sequences is low. Cheers Anna

Date: Tue, 1 Mar 2011 14:31:22 +0000 (GMT) From: Marco Sette m77it@yahoo.it Subject: [modeller_usage] No template... To: modeller modeller_usage@salilab.org Message-ID: 286694.64907.qm@web24003.mail.ird.yahoo.com Content-Type: text/plain; charset=iso-8859-1

Dear all,

I have a protein consisting of a C-terminal and N-terminal region. While for the C-terminal one I have a good template either Modeller or Blast don't suggest templates for the N-terminal one. I have some suggestion using Modweb (which search performs Modweb?) but not very good. Could ou suggest me a website to search for a template? I looked at the mailing list (very long...) but seems this question has not been posed. Many thanks,

Marco

Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328

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End of modeller_usage Digest, Vol 10, Issue 41 **********************************************