Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions

A S Siddiqui, G J Barton

Research output: Contribution to journalArticle

144 Citations (Scopus)

Abstract

An algorithm is presented for the fast and accurate definition of protein structural domains from coordinate data without prior knowledge of the number or type of domains. The algorithm explicitly locates domains that comprise one or two continuous segments of protein chain. Domains that include more than two segments are also located. The algorithm was applied to a nonredundant database of 230 protein structures and the results compared to domain definitions obtained from the literature, or by inspection of the coordinates on molecular graphics. For 70% of the proteins, the derived domains agree with the reference definitions, 18% show minor differences and only 12% (28 proteins) show very different definitions. Three screens were applied to identify the derived domains least likely to agree with the subjective definition set. These screens revealed a set of 173 proteins, 97% of which agree well with the subjective definitions. The algorithm represents a practical domain identification tool that can be run routinely on the entire structural database. Adjustment of parameters also allows smaller compact units to be identified in proteins.

Original languageEnglish
Pages (from-to)872-84
Number of pages13
JournalProtein Science
Volume4
Issue number5
DOIs
Publication statusPublished - May 1995

Keywords

  • Actins
  • Algorithms
  • Computer Graphics
  • Databases, Factual
  • Molecular Structure
  • Protein Conformation
  • Protein Structure, Tertiary
  • Proteins
  • Software
  • Trypsin

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