FAST SIMILARITY SEARCH FOR PROTEIN 3D STRUCTURES USING TOPOLOGICAL PATTERN MATCHING BASED ON SPATIAL RELATIONS

• DOI: 10.1142/s0129065705000244
• Publication Date: 2005-09-23T06:42:07Z
• Authors: SUNG-HEE PARK; KEUN HO RYU; DAVID GILBERT
• Keywords: Similarity (geometry)

Similarity search for protein 3D structures become complex and computationally expensive due to the fact that size of structure databases continues grow tremendously. Recently, fast structural similarity systems have been required put them into practical use in classification whilst existing comparison do not provide results on time. Our approach uses multi-step processing composes a preprocessing step represent geometry with spatial objects, filter generate small candidate set using approximate topological string matching, refinement compute alignment. This paper describes filtering discovery patterns secondary elements based relations. system is fully implemented by Oracle 8i spatial. We previously shown our has advantage speed performance compared other such as DALI. work shows relations proteins.