Fast filtering of structural similarity search using discovery of topological patterns

Abstract

Similarity search for protein 3D structure databases is much more complex and computationally expensive. It is essential to improve performance on the existing comparison systems such as DALI and VAST. In our approach, the structural similarity search composes of a filter step to generate small candidate set and a refinement step to compute structural alignment. This paper describes fast filtering of similarity search using discovery of topological patterns of secondary structure elements based on spatial relations. Our system is fully implemented by using Oracle 8i spatial. Experimental results show that our method is approximately three times faster than DaliLite. © Springer-Verlag Berlin Heidelberg 2004.