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 <[log in to unmask]> 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: [log in to unmask]
> Ph: 215-358-2012
> Fax: 215-358-2020
----------------------------------------------
Kornelius Zeth
Max Planck Institute for Developmental Biology
Dept. Protein Evolution
Spemannstr. 35
72076 Tuebingen, Germany
[log in to unmask]
Tel -49 7071 601 323
Fax -49 7071 601 349
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