| BetaDock: Shape-Priority Docking Method Based on Beta-Complex. | |
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MedLine Citation:
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PMID: 21696235 Owner: NLM Status: In-Data-Review |
Abstract/OtherAbstract:
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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 b-complex. Given the Voronoi diagram of the receptor whose topology is stored in the quasi-triangulation, the b-complex corresponding to water molecule is computed. Then, the boundary of the b-complex defines the b-shape which has the complete proximity information among all atoms on the receptor boundary. From the b-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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Authors:
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D-S Kim; C-M Kim; C-I Won; J-K Kim; J Ryu; Y Cho; C Lee; J Bhak |
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Publication Detail:
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Type: Journal Article |
Journal Detail:
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Title: Journal of biomolecular structure & dynamics Volume: 29 ISSN: 1538-0254 ISO Abbreviation: J. Biomol. Struct. Dyn. Publication Date: 2011 Aug |
Date Detail:
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Created Date: 2011-06-23 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 8404176 Medline TA: J Biomol Struct Dyn Country: United States |
Other Details:
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Languages: eng Pagination: 219-42 Citation Subset: IM |
Affiliation:
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Department of Industrial Engineering, Hanyang University, Seoul, South Korea. dskim@hanyang.ac.kr. |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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