structural alignment services

1topofit	example	paper	it seems this one will consider side chain atoms.
2multiprot		paper	MultiProt finds the common geometrical cores between input molecules.
3POSA	example	Bioinformatics, 2005 21(10):2362-2369	can tell you the core, and also tell you what's in common and what's different between groups.
4MASS	example		align by secondary structure
4SSM	as Dr. Shibata shows you	papers	align by secondary structure