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Hi, With 20% identity the main problem is the sequence alignment. Usually programs that based only sequence data are not enough in such cases and you need to add additional terms to get the "correct" structure (e.g. threading). You can see list of such programs in our site http://bip.weizmann.ac.il/toolbox/structure/3d.htm Try also to work on the sequence alignment by doing multiple sequence alignment (and not just pair alignment) for selected group of sequences. You can use for that programs like TCoffee packege (http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi) , Consensus Server (http://structure.bu.edu/cgi-bin/consensus/ consensus.cgi) and maybe to add structural information to the alignment (e.g. predicted secondary structure) like in Promals3D (http://prodata.swmed.edu/promals3d/promals3d.php) after you have good alignment, the building is straight forward in any homology building program. Gap and insertion are usually in protein loops and they will be always the weak part of your building Good Luck Rotem On 5 May, 2009, at 12:08, Anastassis Perrakis wrote: >>> Suppose I have two proteins A and B, they are structurally >>> homologous, >>> however the sequence identity is only about 20%. A has crystal >>> structure available, so if I want to model protein B, what's the >>> best >>> way to do it? I don't think I can just thread the sequence of B to A >>> structure because the number of residues are different and there >>> might >>> be gaps and insertions in the alignment. Any suggestions of good >>> programs? >>> >> >> >> -- >> Yu Wai Chen, PhD........................................Lecturer >> King's College London, Randall Division +44-207-848-8206 >> New Hunt's House, Guy's Campus, London SE1 1UL, U.K. > > P please don't print this e-mail unless you really need to > Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member > Department of Biochemistry (B8) > Netherlands Cancer Institute, > Dept. B8, 1066 CX Amsterdam, The Netherlands > Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 > 597791 > > > > ------------------------------------------------------------------------ ----------- Rotem Sertchook, Ph.D. Bioinformatics Unit, Biological Services Weizmann Institute of Science, Rehovot 76100, Israel. ------------------------------------------------------------------------ ----------------