HIGH DIMENSIONAL INDEXING FOR PROTEIN STRUCTURE MATCHING USING BOWTIES

ZI H HUANG, XIAOFANG ZHOU, DAWEI SONG
2005 Proceedings of the 3rd Asia-Pacific Bioinformatics Conference  
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
more » ... 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.
doi:10.1142/9781860947322_0003 fatcat:a26fptu53zcn3l4hvd56rka6ta