[ssml] Structure based multiple sequence alignment

[rfsouza at cecm.usp.br]

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