I want to introduce you to MASS, an application for multiple
structural alignment, developed at Tel-Aviv University, Israel.
The site (also for downloading): http://bioinfo3d.cs.tau.ac.il/MASS
MASS (Multiple Alignment by Secondary Structures) is an efficient
method for multiple alignment of protein structures and detection of
structural motifs. Exploiting the secondary structure representation
aids in filtering out noisy results and in making the method highly
efficient and robust. MASS disregards the sequence order of the
secondary structure elements. Thus, it can find non-sequential and
even non-topological structural motifs. An important novel feature of
MASS is subset alignment detection: It does not require that all the
input molecules be aligned. Rather, MASS is capable of detecting
structural motifs shared only by a subset of the molecules.