[ssml] Structure based multiple sequence alignment

[Dan Bolser]

On Tue, 17 May 2005 sangeeta at bioinfo.ernet.in wrote:

>Hi Robson,
>*If* you have a large enough set of the 3D structures of the proteins of
>your interest, you may try a structural alignment of those which will give
>the corresponding sequence alignment also. You may take a look at STRAP
>available at http://www.charite.de/bioinf/strap/ OR CE at
>http://cl.sdsc.edu/ce.html

In general how can a single structure be used to improve a multiple
sequence alignment (if at all)?


>
>Hope this helps.
>Best wishes,
>Sangeeta Sawant
>Bioinformatics Centre
>University of Pune
>India
>
>> Hi everybody,
>>
>> I'm trying to perform some analysis about residue variability on some
>> cell division proteins, looking for conserved sites which might be
>> involved
>> in protein-protein interactions. In order to do this, I'm using methods
>> like
>> evolutionary trace and the methods implemented on the Consurf server.
>>
>> My first round of analysis seems to indicate that such methods are very
>> sensible to differences in input multiple sequence alignments, since they
>> use the variation in an alignment column to identify highly conserved
>> residues. Therefore, hoping to improve the matching of homologous residues
>> to alignment columns, I'm looking for a tool that is able to build
>> multiple
>> protein sequence alignments using strutural information, which is
>> available
>> for some of my sequences in PDB.
>>
>> Do you know if there is any alignment program that multiply aligns
>> a set of homologous sequences while respecting the best "fit" of those
>> sequences to a 3D structure?
>>
>> Thanks for any help.
>> Best,
>> Robson
>>
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>
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