[BiO BB] hi
Gary Van Domselaar
gary at www.bioinformatics.org
Tue Jan 6 11:48:53 EST 2004
Hi Pankaj,
I know of a commercial software product than can combines structure and
sequence information to do mulitple alignments: MOE, developed by the
chemical computing group. I think they have educational versions
available for a reduced cost, or maybe even free. Try:
http://www.chemcomp.com/
They a have an article available on their alignment algorithm:
http://www.chemcomp.com/Journal_of_CCG/Features/align.htm
Hope that helps.
Regards,
g.
On Tue, 6 Jan 2004, Pankaj wrote:
> hi all,
> i m a new member of this board.
> i have a 3 protein structures (all taking the same fold) with the
> substrate bound. the residues surrounding the substrate are the active
> site residues. now i have a set of 400 protein sequences which i know
> take the same above mentioned fold. i want to extract the active site
> residues from these 400 sequences. but whatever alignment program i
> use either uses only sequence information or only structure
> information. is there an alignment program which can use both
> structure and sequence information for the alignment of these 400
> sequences on the strcutural template
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