<Shameless self-promoting plugin warning>
Our meta-tool for construct design:
http://xtal.nki.nl/ccd/Welcome.html
More or less similar to what Kornelius showed, but skipping the
alignments
(since most secondary prediction tools do that internally anyway)
plus it lets you choose your starts and ends, and it also designs
primers for your PCR
(since we use the DNA sequence as input and translate)
Tassos
</Shameless self-promoting plugin warning>
On Mar 30, 2009, at 15:29, Kornelius Zeth wrote:
Hi -
we normally use:
http://toolkit.tuebingen.mpg.de/hhpred
together with:
http://toolkit.tuebingen.mpg.de/quick2_d
Both routines have a nice interface and a very sensitive and novel
CS-Blast algorithm which can be used/integrated into the search.
Best wishes
Kornelius
On Mon, 30 Mar 2009 14:11:02 +0100
Haridasan Namboodiri <vnambood...@locuspharma.com> wrote:
Hello
I am designing a protein construct for structural biology. It is a
protein kinase
which has not been crystallized earlier. I was comparing the kinase
domains of
other closely related family members characterized biochemically vs
crystallization constructs. For crystallography constructs, there
are different
stretches of amino acid residues particularly at the N-terminus
(some contain
extra 2-5 residues while others have 15-20 residues.
My question: Is there a rational way of designing exact
constructs one
would propose to make, eg., by a sequence alignment showing nearest
homology neighbors that guided construct design etc..
Sincerely
Hari
Haridasan V. M. Namboodiri, PhD
Scientist-Structural Biology
Locus Pharmaceuticals, Inc.
Four Valley Square
512 Township Line Road
Blue Bell, PA 19422
email: vnambood...@locuspharma.com
Ph: 215-358-2012
Fax: 215-358-2020
----------------------------------------------
Kornelius Zeth
Max Planck Institute for Developmental Biology
Dept. Protein Evolution
Spemannstr. 35
72076 Tuebingen, Germany
kornelius.z...@tuebingen.mpg.de
Tel -49 7071 601 323
Fax -49 7071 601 349
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
