Paper Title:
A Method of Structure Comparison Using Spatial Topological Patterns
  Abstract

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.

  Info
Periodical
Key Engineering Materials (Volumes 277-279)
Edited by
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
Pages
272-277
DOI
10.4028/www.scientific.net/KEM.277-279.272
Citation
S. H. Park, K. H. Ryu, "A Method of Structure Comparison Using Spatial Topological Patterns", Key Engineering Materials, Vols. 277-279, pp. 272-277, 2005
Online since
January 2005
Export
Price
$32.00
Share

In order to see related information, you need to Login.

In order to see related information, you need to Login.

Authors: Ren Feng Li, Xiang Qin Tian, Kun Zhao, Jin Qing Jiang, San Hu Wang
Chapter 1: Material Science
Abstract:The transferring(Tf) receptor from Actinobacillus pleuropneumoniae (App) is comprised of a surface exposed lipoprotein, Tf-binding protein B...
256
Authors: Xin Chen, Long Shao, Ming Wei Lv, Qian Yu
Chapter 4: Biomedical Manufacturing
Abstract:PSO has slow convergence speed and low precision. In this paper, we combine Particle Swarm Optimization (PSO) and levy flight for the task of...
435
Authors: Ru Xiong, Yong Zai Lu, Xuan Hao Zhou, Wei Hua Xu
Chapter 1: Materials and Mechanical Engineering
Abstract:Due to the critical positions of the studies of protein folding in medical and biological systems, the intelligent computation has been...
40
Authors: Shi Gang Wang, Feng Juan Wang, Shu Feng Jiang, Hong Jun Zhang
Chapter 15: Software and Computer in Research and Engineering Solutions
Abstract:Protein structure prediction occupies an important position on bioinformatics science. In this paper, basic theory of particle swarm...
2497
Authors: Ting Wen, An Chun Cheng, Ming Shu Wang
Chapter 3: Biochemical, Medicine Engineering and Technologies, Applications of Genetic Engineering
Abstract:Previous studies indicate that the UL17 protein and its homology play similar roles in viral DNA cleavage and packaging of herpesviruses....
638