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BetaDock: Shape-Priority Docking Method Based on Beta-Complex

Title
BetaDock: Shape-Priority Docking Method Based on Beta-Complex
Author
김재관
Keywords
Voronoi diagram of spheres; Quasi-triangulation; Beta-complex; Beta-shape; AutoDock; Singular value decomposition; Assignment problem; Energy optimization; PROTEIN-LIGAND DOCKING; MOLECULAR-SURFACE RECOGNITION; AIDS DRUG DESIGN; AUTOMATED DOCKING; GENETIC ALGORITHM; FLEXIBLE DOCKING; VORONOI-DIAGRAM; BINDING-SITE; 3-DIMENSIONAL STRUCTURE; GLOBAL OPTIMIZATION
Issue Date
2011-05
Publisher
ADENINE PRESS, 2066 CENTRAL AVE, SCHENECTADY, NY 12304 USA
Citation
Journal of biomolecular structure ' dynamics, Vol.29 No.1 [2011], 219-242
Abstract
This paper presents an approach and a software. Beta Dock, to the docking problem by putting the priority on shape complementarity between a receptor and a ligand. The approach is based on the theory of the beta-complex. Given the Voronoi diagram of the receptor whose topology is stored in the quasi-triangulation, the beta-complex corresponding to water molecule is computed. Then, the boundary of the beta-complex defines the beta-shape which has the complete proximity information among all atoms on the receptor boundary. From the beta-shape, we first compute pockets where the ligand may bind. Then, we quickly place the ligand within each pocket by solving the singular value decomposition problem and the assignment problem. Using the conformations of the ligands within the pockets as the initial solutions, we run the genetic algorithm to find the optimal solution for the docking problem. The performance of the proposed algorithm was verified through a benchmark test and showed that Beta Dock is superior to a popular docking software AutoDock 4.
URI
http://www.tandfonline.com/doi/abs/10.1080/07391102.2011.10507384http://hdl.handle.net/20.500.11754/37724
ISSN
0739-1102; 1538-0254
DOI
10.1080/07391102.2011.10507384
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ETC[S] > 연구정보
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