[ssml] Structure based multiple sequence alignment

[sangeeta at bioinfo.ernet.in]

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

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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