Support vector machines for prediction and analysis of beta and gamma-turns in proteins

J Bioinform Comput Biol. 2005 Apr;3(2):343-58. doi: 10.1142/s0219720005001089.

Abstract

Tight turns have long been recognized as one of the three important features of proteins, together with alpha-helix and beta-sheet. Tight turns play an important role in globular proteins from both the structural and functional points of view. More than 90% tight turns are beta-turns and most of the rest are gamma-turns. Analysis and prediction of beta-turns and gamma-turns is very useful for design of new molecules such as drugs, pesticides, and antigens. In this paper we investigated two aspects of applying support vector machine (SVM), a promising machine learning method for bioinformatics, to prediction and analysis of beta-turns and gamma-turns. First, we developed two SVM-based methods, called BTSVM and GTSVM, which predict beta-turns and gamma-turns in a protein from its sequence. When compared with other methods, BTSVM has a superior performance and GTSVM is competitive. Second, we used SVMs with a linear kernel to estimate the support of amino acids for the formation of beta-turns and gamma-turns depending on their position in a protein. Our analysis results are more comprehensive and easier to use than the previous results in designing turns in proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Amino Acids / chemistry*
  • Artificial Intelligence*
  • Cluster Analysis
  • Computer Simulation
  • Models, Chemical
  • Models, Molecular*
  • Molecular Sequence Data
  • Pattern Recognition, Automated / methods*
  • Protein Structure, Secondary
  • Proteins / analysis
  • Proteins / chemistry*
  • Proteins / classification
  • Sequence Alignment / methods
  • Sequence Analysis, Protein / methods*

Substances

  • Amino Acids
  • Proteins