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High dimensional indexing for protein structure matching using bowties.

Huang, Zi H.; Zhou, Xiaofang; Song, Dawei

Authors

Zi H. Huang

Xiaofang Zhou

Dawei Song



Contributors

Yi-Ping Phoebe Chen
Editor

Limsoon Wong
Editor

Abstract

For determining functionality dependencies between two proteins, both represented as 3D structures, it is an essential condition that they have a matching structure. As 3D structures for proteins are large, complex and constantly evolving, it is very time-consuming to identify possible locations and sizes of such a matching structure for a given protein against a large protein database. In this paper, we introduce a novel representation model and apply a transformation and formalization to this problem. We then propose a database solution by using innovative high dimensional indexing mechanisms. Experimental results demonstrate a promising performance of the high dimensional indexing to this biologically critical but previously computationally prohibitive problem.

Citation

HUANG, Z.H., ZHOU, X. and SONG, D. 2005. High dimensional indexing for protein structure matching using bowties. In Chen, Y.-P.P. and Wong, L. (eds.) Proceedings of the 3rd Asia-Pacific bioinformatics conference (APBC'05), 17-21 January 2005, Singapore. Advances in bioinformatics and computational biology, 1. London: Imperial College Press [online], pages 21-30. Available from: https://doi.org/10.1142/9781860947322_0003

Conference Name 3rd Asia-Pacific bioinformatics conference (APBC'05)
Conference Location Singapore
Start Date Jan 17, 2005
End Date Jan 21, 2005
Acceptance Date Jan 31, 2005
Online Publication Date Jan 31, 2005
Publication Date Jan 31, 2005
Deposit Date Aug 27, 2009
Publicly Available Date Aug 27, 2009
Publisher Imperial College Press
Pages 21-30
Series Title Advances in bioinformatics and computational biology
Series Number 1
ISBN 1860944779; 9781860944772
DOI https://doi.org/10.1142/9781860947322_0003
Keywords Protein structures High dimensional indexing
Public URL http://hdl.handle.net/10059/408

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