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Probabilistic expression of spatially varied amino acid dimers into general form of Chou's pseudo amino acid composition for protein fold recognition

Saini, Harsh and Raicar, Gaurav and Sharma, Alokanand and Lal, Sunil P. and Dehzangi, A. and Lyons, J. and Paliwal, K.K. and Imoto, S. and Miyano, S. (2015) Probabilistic expression of spatially varied amino acid dimers into general form of Chou's pseudo amino acid composition for protein fold recognition. Journal of Theoretical Biology, 380 . pp. 291-298. ISSN 0022-5193

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    Abstract

    Background Identification of the tertiary structure (3D structure) of a protein is a fundamental problem in biology which helps in identifying its functions. Predicting a protein׳s fold is considered to be an intermediate step for identifying the tertiary structure of a protein. Computational methods have been applied to determine a protein׳s fold by assembling information from its structural, physicochemical and/or evolutionary properties. Methods In this study, we propose a scheme in which a feature extraction technique that extracts probabilistic expressions of amino acid dimers, which have varying degree of spatial separation in the primary sequences of proteins, from the Position Specific Scoring Matrix (PSSM). SVM classifier is used to create a model from extracted features for fold recognition. Results The performance of the proposed scheme is evaluated against three benchmarked datasets, namely the Ding and Dubchak, Extended Ding and Dubchak, and Taguchi and Gromiha datasets. Conclusions The proposed scheme performed well in the experiments conducted, providing improvements over previously published results in literature.

    Item Type: Journal Article
    Subjects: Q Science > Q Science (General)
    Q Science > QA Mathematics > QA75 Electronic computers. Computer science
    Divisions: Faculty of Science, Technology and Environment (FSTE) > School of Computing, Information and Mathematical Sciences
    Faculty of Science, Technology and Environment (FSTE)
    Faculty of Science, Technology and Environment (FSTE) > School of Engineering and Physics
    Depositing User: Harsh Saini
    Date Deposited: 22 Jun 2015 11:56
    Last Modified: 23 May 2016 09:10
    URI: http://repository.usp.ac.fj/id/eprint/8323
    UNSPECIFIED

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