I recommend Swiss Pro's Deep View for homology modeling with a single template. You should use VAST searching for the most diverse sequences to find suitable pdb homologs. Best to align your protein sequence with the choices from VAST, being careful to align turns (pro's, gly's etc) and if you have gaps put them at the end or beginning of helices or strands. With evolution, strands are usually stay strands and helices stay helical, but may lengthen or shorten. Modeler is the the most advanced program but not the most intuitive. Both are free to academics.
Dr. Paul Kraft Adjunct Professor of Biochemistry Structural Biologist cell 586-596-2770 email: [email protected] ----- Forwarded Message ----- From: amro selem <[email protected]> To: [email protected] Sent: Friday, August 24, 2012 4:24 PM Subject: [ccp4bb] structural homology Dear all, i want to do structural homology but i am still beginner , could some one help me to do it.is there are specific programs to do that or should i do it manually ? thank you Amr
