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ICML
2007
IEEE

Structural alignment based kernels for protein structure classification

10 years 5 days ago
Structural alignment based kernels for protein structure classification
Structural alignments are the most widely used tools for comparing proteins with low sequence similarity. The main contribution of this paper is to derive various kernels on proteins from structural alignments, which do not use sequence information. Central to the kernels is a novel alignment algorithm which matches substructures of fixed size using spectral graph matching techniques. We derive positive semi-definite kernels which capture the notion of similarity between substructures. Using these as base more sophisticated kernels on protein structures are proposed. To empirically evaluate the kernels we used a 40% sequence non-redundant structures from 15 different SCOP superfamilies. The kernels when used with SVMs show competitive performance with CE, a state of the art structure comparison program.
Sourangshu Bhattacharya, Chiranjib Bhattacharyya,
Added 17 Nov 2009
Updated 17 Nov 2009
Type Conference
Year 2007
Where ICML
Authors Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma Chandra
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