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.
------------------------------------------------------------------------
----------------
