Acta Crystallographica Section D

Biological Crystallography

Volume 60, Part 12 Number 1 (December 2004)

research papers

Acta Cryst. (2004). D60, 2256-2268 [ doi:10.1107/S0907444904026460 ]

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

E. Krissinel and K. Henrick

Abstract: The present paper describes the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone C $_\alpha$ atoms. The SSM results are compared with those obtained from other protein comparison servers, and the advantages and disadvantages of different scores that are used for structure recognition are discussed. A new score, balancing the r.m.s.d. and alignment length $N_{\rm align}$ , is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and $N_{\rm align}$ .

Keywords: secondary-structure matching (SSM); three-dimensional protein structure comparison.

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