Linked Life Data

21696235

Source:http://linkedlifedata.com/resource/pubmed/id/21696235

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2011-6-23
pubmed:abstractText
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 ?-complex. Given the Voronoi diagram of the receptor whose topology is stored in the quasi-triangulation, the ?-complex corresponding to water molecule is computed. Then, the boundary of the ?-complex defines the ?-shape which has the complete proximity information among all atoms on the receptor boundary. From the ?-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.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
1538-0254
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
29
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
219-42
pubmed:meshHeading
pubmed:year
2011
pubmed:articleTitle
BetaDock: shape-priority docking method based on beta-complex.
pubmed:affiliation
Department of Industrial Engineering, Hanyang University, Seoul, South Korea. dskim@hanyang.ac.kr
pubmed:publicationType
Journal Article