Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence

Dmitrij Frishman, Patrick Argos

Research output: Contribution to journalArticlepeer-review

359 Scopus citations

Abstract

Existing approaches to protein secondary structure prediction from the amino acid sequence usually rely on the statistics of local residue interactions within a sliding window and the secondary structural state of the central residue. The practically achieved accuracy limit of such single residue and single sequence prediction methods is ~65% in three structural stages (α-helix, β-strand and coil). Further improvement in the prediction quality is likely to require exploitation of various aspects of three-dimensional protein architecture. Here we make such an attempt and present an accurate algorithm for secondary structure prediction based on recognition of potentially hydrogen-bonded residues in a single amino acid sequence. The unique feature of our approach involves database-derived statistics on residue type occurrences in different classes of β-bridges to delineate interacting β-strands. The α-helical structures are also recognized on the basis of amino acid occurrences in hydrogen-bonded pairs (i,i+4). The algorithm has a prediction accuracy of 68% in three structural stages, relies only on a single protein sequence as input and has the potential to be improved by 5-7% if homologous aligned sequences are also considered.

Original languageEnglish
Pages (from-to)133-142
Number of pages10
JournalProtein Engineering
Volume9
Issue number2
DOIs
StatePublished - Feb 1996
Externally publishedYes

Keywords

  • Hydrogen bonds
  • Protein fold
  • Protein sequence
  • Protein structure
  • Secondary structure

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