• 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 Cinline image 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 inline image, 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 inline image.