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Comparison of protein structures by growing neighborhood alignments

Bhattacharya, Sourangshu and Bhattacharyya, Chiranjib and Chandra, Nagasuma R (2007) Comparison of protein structures by growing neighborhood alignments. In: BMC Bioinformatics, 8 (77).


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Design of protein structure comparison algorithm is an important research issue, having far reaching implications. In this article, we describe a protein structure comparison scheme, which is capable of detecting correct alignments even in difficult cases, e.g. non-topological similarities. The proposed method computes protein structure alignments by comparing, small substructures, called neighborhoods. Two different types of neighborhoods, sequence and structure, are defined, and two algorithms arising out of the scheme are detailed. A new method for computing equivalences having non-topological similarities from pairwise similarity score is described. A novel and fast technique for comparing sequence neighborhoods is also developed.

Item Type: Journal Article
Publication: BMC Bioinformatics
Publisher: BioMed Central Ltd.
Additional Information: Copyright of this article belongs to BioMed Central Ltd.
Department/Centre: Division of Information Sciences (Doesn't exist now) > BioInformatics Centre
Division of Electrical Sciences > Computer Science & Automation
Date Deposited: 02 Jun 2008
Last Modified: 19 Sep 2010 04:45
URI: http://eprints.iisc.ac.in/id/eprint/14142

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