Protein folding classification by committee SVM array

Abstract

Protein folding classification is a meaningful step to improve analysis of the whole structures. We have designed committee Support Vector Machines (committee SVMs) and their array (committee SVM array) for the prediction of the folding classes. Learning and test data are amino acid sequences drawn from SCOP (Structure Classification Of Protein database). The classification category is compatible with the SCOP. SVMs and committee SVMs are designed in an one-versus-others style both for chemical data and sliding window patterns (spectrum kernels). This generates the committee SVM array. Classification performances are measured in view of the Receiver Operating Characteristic curves (ROC). Superiority of the committee SVM array to existing prediction methods is obtained through extensive experiments to compute the ROCs. © 2009 Springer Berlin Heidelberg.