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http://dx.doi.org/10.9717/kmms.2012.15.6.794

Comparison of Voxel Map and Sphere Tree Structures for Proximity Computation of Protein Molecules  

Kim, Byung-Joo (경북대학교 전자공학과 대학원)
Lee, Jung-Eun (경북대학교 전자전기컴퓨터학부 대학원)
Kim, Young-J. (이화여자대학교 컴퓨터공학전공)
Kim, Ku-Jin (경북대학교 컴퓨터학부)
Publication Information
Journal of Korea Multimedia Society / v.15, no.6, 2012 , pp. 794-804 More about this Journal
Abstract
For the geometric computations on the protein molecules, the proximity queries, such as computing the minimum distance from an arbitrary point to the molecule or detecting the collision between a point and the molecule, are essential. For the proximity queries, the efficiency of the computation time can be different according to the data structure used for the molecule. In this paper, we present the data structures and algorithms for applying proximity queries to a molecule with GPU acceleration. We present two data structures, a voxel map and a sphere tree, where the molecule is represented as a set of spheres, and corresponding algorithms. Moreover, we show that the performance of presented data structures are improved from 3 to 633 times compared to the previous data structure for the molecules containing 1,000~15,000 atoms.
Keywords
Protein Molecule; Proximity Query; Sphere Tree; Voxel Map; Molecular Docking; Molecular Interface;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
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