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Try Phyre (http://www.sbg.bio.ic.ac.uk/phyre/), it worked rather well for some of my projects with very low sequence similarity. Peter On Tue, 5 May 2009 12:08:04 +0300, Anastassis Perrakis <[log in to unmask]> wrote: > Modeller is indeed an excellent program (so are some others) but, > without being an expert, I was told some time ago and I am still under > the impression, that homology modeling with 20% identity (and many > insertions and deletions as you point out) is a dark art. Being able > to suggest the identical fold with some threading algorithm, is likely > all you will be able to do. A homology based model might be too much > to ask. > > A. > > On May 5, 2009, at 11:39, Chen, Yu Wai wrote: > >> I would recommend Modeller >> http://www.salilab.org/modeller/ >> >> Wai >>> 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 -- Peter Schmidtke ---------------------- PhD Student at the Molecular Modeling and Bioinformatics Group Dep. Physical Chemistry Faculty of Pharmacy University of Barcelona