SMOTE based protein fold prediction classification

Abstract

Protein contact maps are two dimensional representations of protein structures. It is well known that specific patterns occuring within contact maps correspond to configurations of protein secondary structures. This paper addresses the problem of protein fold prediction which is a multi-class problem having unbalanced classes. A simple and computationally inexpensive algortihm called Eight-Neighbour algortihm is proposed to extract novel features from the contact map. It is found that of Support Vector Machine (SVM) which can be effectively extended from a binary to a multi-class classifier does not perform well on this problem. Hence in order to boost the performance, boosting algorithm called SMOTE is applied to rebalance the data set and then a decision tree classifier is used to classify "folds" from the features of contact map. The classification is performed across the four major protein structural classes as well as among the different folds within the classes. The results obtained are promising validating the simple methodology of boosting to obtain improved performance on the fold classification problem using features derived from the contact map alone. © 2013 Springer-Verlag.