Protein Fold Recognition Using Self-Organizing Map Neural Network

Abstract

In this work, we propose a solution for the recognition of protein folds using Self-Organizing Map (SOM) neural network and present a comparison between few approaches. We use SOM, Fisher’s Linear Discriminant Analysis (FLD), K-Nearest Neighbor (KNN), Support Vector Machine (SVM) and Multi-Layer Perceptron (MLP) methods for the recognition of three SCOP folds with six attributes (amino acid composition, predicted secondary structure, hydrophobicity, normalized van der Waals volume, polarity and polarizability). Then we classify the most common 27 SCOP folds using 125 dimensional data formed by the six attributes. This paper has a novelty in the way of applying SOM to these six attributes, and also portrays the capabilities of SOM among the other methods in protein fold classification. Firstly for the threeclass problem, the methods are tested on 120 proteins by applying 10-fold cross-validation technique and 93.33% classification performance is obtained with SOM. Secondly for the 27-class problem SOM is tested on 694 proteins by applying one-versus-others technique and 73.37% classification performance is obtained. Keywords: Protein fold recognition, protein fold classification, neural networks, self-organizing map.