High dimensional indexing for protein structure matching

Huang, Zi H.; Zhou, Xiaofang and Song, Dawei (2005). High dimensional indexing for protein structure matching. In: Proceedings of the Third Asia Pacific Bioinformatics Conference (APBC'2005), 17-21 Jan 2005, Singapore.

DOI: https://doi.org/10.1142/9781860947322_0003


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.

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