A neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment.

Kaur, Harpreet and Raghava, G.P.S. (2003) A neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment. Protein science : a publication of the Protein Society, 12 (5). pp. 923-9. ISSN 0961-8368

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Abstract

In the present study, an attempt has been made to develop a method for predicting gamma-turns in proteins. First, we have implemented the commonly used statistical and machine-learning techniques in the field of protein structure prediction, for the prediction of gamma-turns. All the methods have been trained and tested on a set of 320 nonhomologous protein chains by a fivefold cross-validation technique. It has been observed that the performance of all methods is very poor, having a Matthew's Correlation Coefficient (MCC) </= 0.06. Second, predicted secondary structure obtained from PSIPRED is used in gamma-turn prediction. It has been found that machine-learning methods outperform statistical methods and achieve an MCC of 0.11 when secondary structure information is used. The performance of gamma-turn prediction is further improved when multiple sequence alignment is used as the input instead of a single sequence. Based on this study, we have developed a method, GammaPred, for gamma-turn prediction (MCC = 0.17). The GammaPred is a neural-network-based method, which predicts gamma-turns in two steps. In the first step, a sequence-to-structure network is used to predict the gamma-turns from multiple alignment of protein sequence. In the second step, it uses a structure-to-structure network in which input consists of predicted gamma-turns obtained from the first step and predicted secondary structure obtained from PSIPRED.

Item Type:	Article
Additional Information:	Copyright of this article belongs to Wiley.
Uncontrolled Keywords:	�-Turns; prediction; neural networks; Weka classifiers; statistical; multiple alignment; secondary structure; Web server
Subjects:	Q Science > QR Microbiology
Depositing User:	Dr. K.P.S.Sengar
Date Deposited:	06 Jan 2012 14:59
Last Modified:	06 Jan 2012 14:59
URI:	http://crdd.osdd.net/open/id/eprint/246

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