75% Accuracy in Protein Secondary Structure Prediction

  • Frishman D
  • Argos P
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Abstract

In this study we present an accurate secondary structure prediction
procedure by using an query and related sequences. The most novel
aspect of our approach is its reliance on local pairwise alignment
of the sequence to be predicted with each related sequence rather
than utilization of a multiple alignment. The residue-by-residue
accuracy of the method is 75% in three structural states after jack-knife
tests. The gain in prediction accuracy compared with the existing
techniques, which are at best 72%, is achieved by secondary structure
propensities based on both local and long-range effects, utilization
of similar sequence information in the form of carefully selected
pairwise alignment fragments, and reliance on a large collection
of known protein primary structures. The method is especially appropriate
for large-scale sequence analysis of efforts such as genome characterization,
where precise and significant multiple sequence alignments are not
available or achievable.

Author-supplied keywords

  • *Algorithms Amino Acid Sequence Carrier Proteins/c
  • Amino Acid
  • Factual Integration Host Factors *Models
  • Molecular Molecular Sequence Data Protein Conform
  • Secondary Proteins/*chemistry Sequence Alignment/

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Authors

  • D Frishman

  • P Argos

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