Check out Theseus: http://www.theseus3d.org/
You will need a sequence based alignment. This alignment can be provided automatically by muscle if you have it installed (http://www.drive5.com/muscle/)--this is different from pymol. Pymol seems to do an SVD to obtain the alignment. I'm not up to date on what all the other programs are using, but I think most use least-squares, so you need to provide a sequence based alignment for these programs Theseus results are always as good or better (subjectively speaking) than straight least-squares superposition. I don't know how the Theseus/muscle combo compares to pymol's use of SVD in terms of alignment quality because I haven't compared them directly. James On Aug 18, 2011, at 3:10 AM, Suda Ravindran wrote: > Dear all, > > I would like to know the tools/servers/programs that can be used for > structure based superposition of two or more proteins. Please help me out..!! > > Thanks, > > -Suda
