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
