Personal tools
You are here: Home Publications A Novel Method of Protein Secondary Structure Prediction with High Segment Overlap Measure: Support Vector Machine Approach
Document Actions

S. Hua and Z. Sun (2001)

A Novel Method of Protein Secondary Structure Prediction with High Segment Overlap Measure: Support Vector Machine Approach

Journal of Molecular Biology:(in press).

We introduced a new method of protein secondary structure prediction which is based on the theory of Support Vector Machine (SVM). SVM represents a new approach to supervised pattern classification which has been successfully applied to a wide range of pattern recognition problems, including object recognition, speaker identification, gene function prediction with microarray expression profile, etc. In these cases, the performance of SVM either matches or is significantly better than of traditional machine learning approaches, including neural networks. The first use of the SVM approach to predict protein secondary structure is described in this paper. Unlike the previous studies, we first constructed several binary classifiers, then assembled a tertiary classifier for three secondary structure states (helix, sheet and coil) based on these binary classifiers. The SVM method achieved a good performance of Segment Overlap accuracy SOV=76.2% through 7-fold cross validation on a database of 513 non-homologous protein chains, with multiple sequence alignments, which out-performs existing methods. Meanwhile three-state overall per-residue accuracy Q3 achieved 73.5%, which is at least comparable to the existing single prediction method. Furthermore a useful ¡®Reliability Index¡¯ for the predictions was developed. In addition, SVM has many attractive features, including effective avoidance of overfitting, the ability to handle large feature spaces, information condensing of the given data set, etc. The SVM method is conveniently applied to many other pattern classification tasks in biology.

by admin last modified 2007-01-31 11:09

Powered by Plone CMS, the Open Source Content Management System