Identification of functional residues and secondary structure from protein multiple sequence alignment

C D Livingstone, G J Barton

Research output: Contribution to journalArticle

60 Citations (Scopus)

Abstract

This chapter describes a strategy for the hierarchical analysis of residue conservation and the identification of functional residues and secondary structure from protein multiple sequence alignment. Hierarchical methods of alignment cope with large numbers of sequences and give reasonably accurate alignments. Having generated the alignment, the problem is to find out what it can tell us about the protein family. Interpretation of alignments can be, particularly difficult when there are large numbers of sequences to examine. The method allows the residue-specific similarities and differences in physicochemical properties among groups of sequences to be identified quickly. The method also highlights conserved positions across a complete alignment and, thus, can help to identify patterns characteristic of regular secondary structures. The chapter also discusses a procedure for applying these patterns in secondary structure prediction and evaluates their predictive power in six blind secondary-structure predictions.
Original languageEnglish
Pages (from-to)497-512
Number of pages16
JournalMethods in Enzymology
Volume266
DOIs
Publication statusPublished - 1996

Fingerprint

Secondary Protein Structure
Sequence Alignment
Proteins
Conservation

Keywords

  • Amino Acid Sequence
  • Amino Acids
  • Annexins
  • Conserved Sequence
  • Databases, Factual
  • Flavodoxin
  • Molecular Sequence Data
  • Phylogeny
  • Protein Structure, Secondary
  • Proteins
  • Reproducibility of Results
  • Sequence Homology, Amino Acid
  • Software

Cite this

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title = "Identification of functional residues and secondary structure from protein multiple sequence alignment",
abstract = "This chapter describes a strategy for the hierarchical analysis of residue conservation and the identification of functional residues and secondary structure from protein multiple sequence alignment. Hierarchical methods of alignment cope with large numbers of sequences and give reasonably accurate alignments. Having generated the alignment, the problem is to find out what it can tell us about the protein family. Interpretation of alignments can be, particularly difficult when there are large numbers of sequences to examine. The method allows the residue-specific similarities and differences in physicochemical properties among groups of sequences to be identified quickly. The method also highlights conserved positions across a complete alignment and, thus, can help to identify patterns characteristic of regular secondary structures. The chapter also discusses a procedure for applying these patterns in secondary structure prediction and evaluates their predictive power in six blind secondary-structure predictions.",
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Identification of functional residues and secondary structure from protein multiple sequence alignment. / Livingstone, C D; Barton, G J.

In: Methods in Enzymology, Vol. 266, 1996, p. 497-512.

Research output: Contribution to journalArticle

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T1 - Identification of functional residues and secondary structure from protein multiple sequence alignment

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AU - Barton, G J

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KW - Amino Acids

KW - Annexins

KW - Conserved Sequence

KW - Databases, Factual

KW - Flavodoxin

KW - Molecular Sequence Data

KW - Phylogeny

KW - Protein Structure, Secondary

KW - Proteins

KW - Reproducibility of Results

KW - Sequence Homology, Amino Acid

KW - Software

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