gamma-turn types prediction in proteins using the two-stage hybrid neural discriminant model

Abstract

Due to the slightly success of protein secondary structure prediction using the various algorithmic and non-algorithmic techniques, similar techniques have been developed for predicting gamma-turns in proteins by Kaur and Raghava [2003. A neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment. Protein Sci. 12,923-929]. However, the major limitation of previous methods was in ability in predicting gamma-turn types. In a recent investigation we introduced a sequence based predictor model for predicting gamma-turn types in proteins [Jahandideh, S., Sabet Sarvestani, A., Abdolmaleki, P., Jahandideh, M., Barfeie, M, 2007a. gamma-turn types prediction in proteins using the support vector machines. J. Theor. Biol. 249,785-790]. In the present work, in order to analyze the effect of sequence and structure in the formation of gamma-turn types and predicting gamma-turn types in proteins, we applied novel hybrid neural discriminant modeling procedure. As the result, this study clarified the efficiency of using the statistical model preprocessors in determining the effective parameters. Moreover, the optimal structure of neural network can be simplified by a preprocessor in the first stage of hybrid approach, there by reducing the needed time for neural network training procedure in the second stage and the probability of over fitting occurrence decreased and a high precision and reliability obtained in this way. (C) 2009 Elsevier Ltd. All rights reserved.