Subject: Proteins comparison
Ref: <961118084342.ZM12382 at si05.IRCM.UMontreal.CA> in bionet.software
duhaimj at ircm.umontreal.ca ("SI-Johanne Duhaime") wrote:
>>Does it exist a program that would align different protein sequences regarding
>their secondary structure?
If you need 3D-alignments of equal-length but different sequences,
the simplest is to use a RMS method on the backbone section.
One is described in J.Comput.Chem,1995,16,80-90.
If you need general 3D-alignments (no pairwise atomic correspondence is needed),
you can use the method described in J.Chem.Inf.Comput.Sci 1996,36,1038-1049.
I wrote the program. If you are looking for some collaboration, I can
perform the 3D-alignments and compute the maximal common 3D-substructure.
It works also for a family of more than 2 proteins.
Michel Petitjean, Email: petitjean at itodys.jussieu.fr
ITODYS (CNRS, URA34) ptitjean at ccr.jussieu.fr