The limits of protein secondary structure prediction accuracy from multiple sequence alignment

Robert B. Russell, Geoffrey J. Barton

Research output: Contribution to journalLetter

70 Citations (Scopus)

Abstract

The expected best residue-by-residue accuracies for secondary structure prediction from multiple protein sequence alignment have been determined by an analysis of known protein structural families. The results show substantial variation is possible among homologous protein structures, and that 100% agreement is unlikely between a consensus prediction and one member of a protein structural family. The study provides the range of agreement to be expected between a perfect secondary structure prediction from a multiple alignment and each protein within the alignment. The results of this study overcome the difficulties inherent in the use of residue-by-residue accuracy for assessing the quality of consensus secondary structure predictions. The accuracies of recent consensus predictions for the annexins, SH2 domains and SH3 domains fall within the expected range for a perfect prediction.

Original languageEnglish
Pages (from-to)951-957
Number of pages7
JournalJournal of Molecular Biology
Volume234
Issue number4
DOIs
Publication statusPublished - 20 Dec 1993

Keywords

  • Amino acid sequence
  • Consensus sequence
  • Molecular sequence data
  • Multigene family
  • Protein structure, Secondary
  • Proteins
  • Sequence alignment
  • Sequence homology, Amino Acid

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