High dimensional indexing for protein structure matching using bowties.

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

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

• Presentation Conference Type: Conference Paper (published)
• Conference Name: 3rd Asia-Pacific bioinformatics conference (APBC'05)
• 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
• Peer Reviewed: Peer Reviewed
• 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
• Contract Date: Aug 27, 2009