A Method of Structure Comparison Using Spatial Topological Patterns
The problem of comparison of structural similarity has been complex and computationally expensive. The first step to solve comparison of structural similarity in 3D structure databases is to develop fast methods for structural similarity. Therefore, we propose a new method of comparing structural similarity in protein structure databases by using topological patterns of proteins. In our approach, the geometry of secondary structure elements in 3D space is represented by spatial data types and is indexed using Rtrees. Topological patterns are discovered by spatial topology relations based on the Rtree index join. An algorithm for a similarity search compares topological patterns of a query protein with those of proteins in structure databases by the intersection frequency of SSEs. Our experimental results show that the execution time of our method is three times faster than the generally known method DALITE. Our method can generate small candidate sets for more accurate alignment tools such as DALI and SSAP.
Kwang Hwa Chung, Yong Hyeon Shin, Sue-Nie Park, Hyun Sook Cho, Soon-Ae Yoo, Byung Joo Min, Hyo-Suk Lim and Kyung Hwa Yoo
S. H. Park and K. H. Ryu, "A Method of Structure Comparison Using Spatial Topological Patterns", Key Engineering Materials, Vols. 277-279, pp. 272-277, 2005