Predicting β-turns in protein using kernel logistic regression

Biomed Res Int. 2013:2013:870372. doi: 10.1155/2013/870372. Epub 2013 Feb 19.

Abstract

A β-turn is a secondary protein structure type that plays a significant role in protein configuration and function. On average 25% of amino acids in protein structures are located in β-turns. It is very important to develope an accurate and efficient method for β-turns prediction. Most of the current successful β-turns prediction methods use support vector machines (SVMs) or neural networks (NNs). The kernel logistic regression (KLR) is a powerful classification technique that has been applied successfully in many classification problems. However, it is often not found in β-turns classification, mainly because it is computationally expensive. In this paper, we used KLR to obtain sparse β-turns prediction in short evolution time. Secondary structure information and position-specific scoring matrices (PSSMs) are utilized as input features. We achieved Q total of 80.7% and MCC of 50% on BT426 dataset. These results show that KLR method with the right algorithm can yield performance equivalent to or even better than NNs and SVMs in β-turns prediction. In addition, KLR yields probabilistic outcome and has a well-defined extension to multiclass case.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods
  • Databases, Protein
  • Logistic Models*
  • Neural Networks, Computer
  • Probability
  • Protein Structure, Secondary*
  • Proteins / chemistry*
  • Reproducibility of Results
  • Software
  • Support Vector Machine

Substances

  • Proteins