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3D protein structure matching by patch signatures

Huang, Helen; Zhou, Xiaofang; Shen, Heng Tao and Song, Dawei (2006). 3D protein structure matching by patch signatures. In: Not Set ed. Database and Expert Systems Applications. Lecture Notes in Computer Science, Volume 4080/2006. Berlin: Springer, pp. 528–537.

DOI (Digital Object Identifier) Link: http://dx.doi.org/10.1007/11827405
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Abstract

For determining functionality dependencies between two proteins, both represented as 3D structures, it is an essential condition that they have one or more matching structural regions called patches. As 3D structures for proteins are large, complex and constantly evolving, it is computationally expensive and very time-consuming to identify possible locations and sizes of patches for a given protein against a large protein database. In this paper, we address a vector space based representation for protein structures, where a patch is formed by the vectors within the region. Based on our previews work, a compact representation of the patch named patch signature is applied here. A similarity measure of two patches is then derived based on their signatures. To achieve fast patch matching in large protein databases, a match-and-expand strategy is proposed. Given a query patch, a set of small k-sized matching patches, called candidate patches, is generated in match stage. The candidate patches are further filtered by enlarging k in expand stage. Our extensive experimental results demonstrate encouraging performances with respect to this biologically critical but previously computationally prohibitive problem.

Item Type: Book Chapter
ISBN: 3-540-37871-5, 978-3-540-37871-6
Academic Unit/Department: Knowledge Media Institute
Mathematics, Computing and Technology > Computing & Communications
Item ID: 9319
Depositing User: Users 6898 not found.
Date Deposited: 28 Sep 2007
Last Modified: 22 Jun 2012 11:44
URI: http://oro.open.ac.uk/id/eprint/9319
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