Support vector machine for predicting alpha-turn types

Peptides. 2003 Apr;24(4):629-30. doi: 10.1016/s0196-9781(03)00100-1.

Abstract

Tight turns play an important role in globular proteins from both the structural and functional points of view. Of tight turns, beta-turns and gamma-turns have been extensively studied, but alpha-turns were little investigated. Recently, a systematic search for alpha-turns classified alpha-turns into nine different types according to their backbone trajectory features. In this paper, Support Vector Machines (SVMs), a new machine learning method, is proposed for predicting the alpha-turn types in proteins. The high rates of correct prediction imply that that the formation of different alpha-turn types is evidently correlated with the sequence of a pentapeptide, and hence can be approximately predicted based on the sequence information of the pentapeptide alone, although the incorporation of its interaction with the other part of a protein, the so-called "long distance interaction", will further improve the prediction quality.

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Computational Biology / methods*
  • Genetic Vectors
  • Molecular Sequence Data
  • Peptides / chemistry
  • Protein Conformation*
  • Protein Structure, Secondary*
  • Software

Substances

  • Peptides