[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:


They a have an article available on their alignment algorithm:


Hope that helps.



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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