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

Fingerprint

Secondary Protein Structure
Sequence Alignment
src Homology Domains
Proteins
Annexins

Keywords

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

Cite this

@article{87e3dc7c396f47fca5c27208b33126bb,
title = "The limits of protein secondary structure prediction accuracy from multiple sequence alignment",
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.",
keywords = "Amino acid sequence, Consensus sequence, Molecular sequence data, Multigene family, Protein structure, Secondary, Proteins, Sequence alignment, Sequence homology, Amino Acid",
author = "Russell, {Robert B.} and Barton, {Geoffrey J.}",
year = "1993",
month = "12",
day = "20",
doi = "10.1006/jmbi.1993.1649",
language = "English",
volume = "234",
pages = "951--957",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Elsevier",
number = "4",

}

The limits of protein secondary structure prediction accuracy from multiple sequence alignment. / Russell, Robert B.; Barton, Geoffrey J.

In: Journal of Molecular Biology, Vol. 234, No. 4, 20.12.1993, p. 951-957.

Research output: Contribution to journalLetter

TY - JOUR

T1 - The limits of protein secondary structure prediction accuracy from multiple sequence alignment

AU - Russell, Robert B.

AU - Barton, Geoffrey J.

PY - 1993/12/20

Y1 - 1993/12/20

N2 - 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.

AB - 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.

KW - Amino acid sequence

KW - Consensus sequence

KW - Molecular sequence data

KW - Multigene family

KW - Protein structure, Secondary

KW - Proteins

KW - Sequence alignment

KW - Sequence homology, Amino Acid

U2 - 10.1006/jmbi.1993.1649

DO - 10.1006/jmbi.1993.1649

M3 - Letter

VL - 234

SP - 951

EP - 957

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 4

ER -