Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
Acta Crystallographica Section D
Volume 60, Issue 12-1, pages 2256–2268, December 2004
How to Cite
Krissinel, E. and Henrick, K. (2004), Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallographica Section D, 60: 2256–2268. doi: 10.1107/S0907444904026460
- secondary-structure matching (SSM);
- three-dimensional protein structure comparison.
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 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 , 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 .