gamma-Turn types prediction in proteins using the support vector machines

J Theor Biol. 2007 Dec 21;249(4):785-90. doi: 10.1016/j.jtbi.2007.09.002. Epub 2007 Sep 11.

Abstract

Recently, two different models have been developed for predicting gamma-turns in proteins by Kaur and Raghava [2002. An evaluation of beta-turn prediction methods. Bioinformatics 18, 1508-1514; 2003. A neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment. Protein Sci. 12, 923-929]. However, the major limitation of previous methods is inability in predicting gamma-turns types. Thus, there is a need to predict gamma-turn types using an approach which will be useful in overall tertiary structure prediction. In this work, support vector machines (SVMs), a powerful model is proposed for predicting gamma-turn types in proteins. The high rates of prediction accuracy showed that the formation of gamma-turn types is evidently correlated with the sequence of tripeptides, and hence can be approximately predicted based on the sequence information of the tripeptides alone.

MeSH terms

  • Algorithms
  • Aminopeptidases / chemistry
  • Computational Biology / methods
  • Databases, Protein
  • Models, Chemical
  • Protein Structure, Secondary*
  • Proteins / chemistry*

Substances

  • Proteins
  • Aminopeptidases
  • PepT tripeptidase