articleActa Crystallographica Section D Biological CrystallographyNov 26, 2004HYBRID OA

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

EKEugene KrissinelKHK. Henrick

European Bioinformatics Institute

PubMed
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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 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.

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Topics & keywords

Topics
Keywords
  • Matching (statistics)
  • Server
  • Computer science
  • Algorithm
  • Structural alignment
  • Protein secondary structure
  • Protein structure
  • Mathematics
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