MESSM: a framework for protein fold recognition using neural networks and support vector machines.

Mitchell, Ian ORCID: https://orcid.org/0000-0002-3882-9127, Jiang, Nan and Wu, Wendy Xinyu (2006) MESSM: a framework for protein fold recognition using neural networks and support vector machines. International Journal of Bioinformatics Research and Applications, 2 (4) . pp. 381-393. ISSN 1744-5493 [Article] (doi:10.1504/IJBRA.2006.011037)

Abstract

This paper presents the results of a PhD project that developed a framework, known as MESSM, for protein fold recognition. The framework has 3 key features: i) an environment-specific amino acid substitution is generated, ii) a mixed substitution mapping is performed by linearly combining the structurally derived substitution mapping with a sequence profile from well-developed amino acid substitution matrices, iii) Support Vector Machines are employed to measure the significance of the sequence-structure alignment. Tested on benchmark problems, MESSM was shown to lead to a better performance of alignment accuracy.

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