MASS 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.
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O. Dror, H. Benyamini, R. Nussinov, and H. Wolfson .
MASS: Multiple structural alignment by secondary structures.
Bioinformatics, 19 Suppl. 1: i95 i104, 2003.