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Shamim, M.T.A. and Anwaruddin, M. and Nagarajaram, H.A. (2007) Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs. Bioinformatics, 23 (24). pp. 3320-3327. ISSN 1367-4803

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Abstract

MOTIVATION: Fold recognition is a key step in the protein structure discovery process, especially when traditional sequence comparison methods fail to yield convincing structural homologies. Although many methods have been developed for protein fold recognition, their accuracies remain low. This can be attributed to insufficient exploitation of fold discriminatory features. RESULTS: We have developed a new method for protein fold recognition using structural information of amino acid residues and amino acid residue pairs. Since protein fold recognition can be treated as a protein fold classification problem, we have developed a Support Vector Machine (SVM) based classifier approach that uses secondary structural state and solvent accessibility state frequencies of amino acids and amino acid pairs as feature vectors. Among the individual properties examined secondary structural state frequencies of amino acids gave an overall accuracy of 65.2% for fold discrimination, which is better than the accuracy by any method reported so far in the literature. Combination of secondary structural state frequencies with solvent accessibility state frequencies of amino acids and amino acid pairs further improved the fold discrimination accuracy to more than 70%, which is approximately 8% higher than the best available method. In this study we have also tested, for the first time, an all-together multi-class method known as Crammer and Singer method for protein fold classification. Our studies reveal that the three multi-class classification methods, namely one versus all, one versus one and Crammer and Singer method, yield similar predictions. AVAILABILITY: Dataset and stand-alone program are available upon request.

Item Type: Article
Depositing User: Dr P Divakar
Date Deposited: 12 Aug 2015 09:59
Last Modified: 12 Aug 2015 09:59
URI: http://cdfd.sciencecentral.in/id/eprint/327

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