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

Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2256-68. doi: 10.1107/S0907444904026460. Epub 2004 Nov 26.


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 Calpha 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 Nalign, 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 Nalign.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Internet
  • Models, Molecular
  • Protein Conformation
  • Protein Structure, Secondary*
  • Proteins / chemistry*
  • Quality Control
  • Software*


  • Proteins