Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
2009-1-15
pubmed:abstractText
Many available methods aimed at incorporating the receptor flexibility in ligand docking are computationally expensive, require a high level of user intervention, and were tested only on benchmarks of limited size and diversity. Here we describe the four-dimensional (4D) docking approach that allows seamless incorporation of receptor conformational ensembles in a single docking simulation and reduces the sampling time while preserving the accuracy of traditional ensemble docking. The approach was tested on a benchmark of 99 therapeutically relevant proteins and 300 diverse ligands (half of them experimental or marketed drugs). The conformational variability of the binding pockets was represented by the available crystallographic data, with the total of 1113 receptor structures. The 4D docking method reproduced the correct ligand binding geometry in 77.3% of the benchmark cases, matching the success rate of the traditional approach but employed on average only one-fourth of the time during the ligand sampling phase.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-10398408, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-10592235, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-10648630, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-11327774, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-11394736, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-11746701, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-12133719, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-12825943, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-12838268, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-12871062, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-15001363, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-15046985, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-15161930, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-15576021, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-15576027, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-15608167, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-15757999, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-15857113, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-15857117, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-15974595, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-15984891, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-16286078, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-16307879, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-17024701, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-17096427, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-17300160, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-17305329, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-17555316, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-18037925, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-18048412, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-18174917, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-18253700, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-18273556, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-18302984, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-18385684, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-18558668, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-591813, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-8090707, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-8289329, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-8742735, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-8780787, http://linkedlifedata.com/resource/pubmed/commentcorrection/19090659-9047373
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jan
pubmed:issn
1520-4804
pubmed:author
pubmed:issnType
Electronic
pubmed:day
22
pubmed:volume
52
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
397-406
pubmed:dateRevised
2011-5-24
pubmed:meshHeading
pubmed:year
2009
pubmed:articleTitle
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking.
pubmed:affiliation
Department of Molecular Biology, The Scripps Research Institute, TPC28, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
pubmed:publicationType
Journal Article, Research Support, N.I.H., Extramural