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Bhak, Jong
KOrean GenomIcs Center(KOGIC)
Research Interests
  • Geromics, genomics, bioinformatics, protein Engineering, OMICS

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

Cited 13 times inthomson ciCited 11 times inthomson ci
Title
BetaDock: Shape-Priority Docking Method Based on Beta-Complex
Author
Kim, Deok-SooKim, Chong-MinWon, Chung-InKim, Jae-KwanRyu, JoonghyunCho, YoungsongLee, ChangheeBhak, Jong Hwa
Keywords
Assignment problem; AutoDock; Beta-complex; Beta-shape; Energy optimization; Quasi-triangulation; Singular value decomposition; Voronoi diagram of spheres
Issue Date
2011-08
Publisher
TAYLOR & FRANCIS INC
Citation
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, v.29, no.1, pp.219 - 242
Abstract
This paper presents an approach and a software, BetaDock, 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 β-complex. Given the Voronoi diagram of the receptor whose topology is stored in the quasi-triangulation, the β-complex corresponding to water molecule is computed. Then, the boundary of the β-complex defines the β-shape which has the complete proximity information among all atoms on the receptor boundary. From the β-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 BetaDock is superior to a popular docking software AutoDock 4.
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ISSN
0739-1102
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BME_Journal Papers
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