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High dimensional indexing for protein structure matching using bowties.

Huang, Z.H.; Zhou, X.; Song, D.


Z.H. Huang

X. Zhou

D. Song


Yi-Ping Phoebe Chen

Limsoon Wong


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.

Start Date Jan 17, 2005
Publication Date Dec 31, 2005
Publisher New Publisher Required
Pages 21-30
Series Title Advances in bioinformatics and computational biology
Series Number 1
ISBN 9781860944772
Institution 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:
Keywords Protein structures High dimensional indexing


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