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Open Access Highly Accessed Research article

A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition

Alok Sharma13*, Kuldip K Paliwal2, Abdollah Dehzangi2, James Lyons2, Seiya Imoto1 and Satoru Miyano1

Author Affiliations

1 Laboratory of DNA Information Analysis, University of Tokyo, Minato-ku, Tokyo, Japan

2 School of Engineering, Griffith University, Brisbane, Australia

3 School of Engineering and Physics, University of the South Pacific, Suva, Fiji

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BMC Bioinformatics 2013, 14:233  doi:10.1186/1471-2105-14-233

Published: 24 July 2013

Abstract

Background

Assigning a protein into one of its folds is a transitional step for discovering three dimensional protein structure, which is a challenging task in bimolecular (biological) science. The present research focuses on: 1) the development of classifiers, and 2) the development of feature extraction techniques based on syntactic and/or physicochemical properties.

Results

Apart from the above two main categories of research, we have shown that the selection of physicochemical attributes of the amino acids is an important step in protein fold recognition and has not been explored adequately. We have presented a multi-dimensional successive feature selection (MD-SFS) approach to systematically select attributes. The proposed method is applied on protein sequence data and an improvement of around 24% in fold recognition has been noted when selecting attributes appropriately.

Conclusion

The MD-SFS has been applied successfully in selecting physicochemical attributes of the amino acids. The selected attributes show improved protein fold recognition performance.