Document Detail


Consensus docking: improving the reliability of docking in a virtual screening context.
MedLine Citation:
PMID:  23351099     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Structure-based virtual screening relies on scoring the predicted binding modes of compounds docked into the target. Because the accuracy of this scoring relies on the accuracy of the docking, methods that increase docking accuracy are valuable. Here, we present a relatively straightforward method for improving the probability of identifying accurately docked poses. The method is similar in concept to consensus scoring schemes, which have been shown to increase ranking power and thus hit rates, but combines information about predicted binding modes rather than predicted binding affinities. The pose prediction success rate of each docking program alone was found in this trial to be 55% for Autodock, 58% for DOCK, and 64% for Vina. By using more than one docking program to predict the binding pose, correct poses were identified in 82% or more of cases, a significant improvement. In a virtual screen, these more reliably posed compounds can be preferentially advanced to subsequent scoring stages to improve hit rates. Consensus docking can be easily introduced into established structure-based virtual screening methodologies.
Authors:
Douglas R Houston; Malcolm D Walkinshaw
Related Documents :
1304319 - In vitro binding of isolated synaptic vesicles to presynaptic plasma membranes: activat...
2948559 - Binding of long-chain alkyl derivatives to lipid bilayers and to (ca2+-mg2+)-atpase.
2819089 - Echinocytosis and microvesiculation of human erythrocytes induced by insertion of meroc...
1973289 - The liposome as a model membrane in correlations of partitioning with alpha-adrenocepto...
21411649 - Trip8b regulates hcn1 channel trafficking and gating through two distinct c-terminal in...
11309399 - Atp-binding cassette transporter a1 (abca1) functions as a cholesterol efflux regulator...
1977749 - Effect of chronic pretreatment of guinea-pigs with beta-adrenoceptor agonists on the na...
14695279 - Comparison of the effect of water release on the interaction of the saccharomyces cerev...
15388159 - Synthesis and biological activities of novel 17-aminogeldanamycin derivatives.
Publication Detail:
Type:  Journal Article     Date:  2013-02-07
Journal Detail:
Title:  Journal of chemical information and modeling     Volume:  53     ISSN:  1549-960X     ISO Abbreviation:  J Chem Inf Model     Publication Date:  2013 Feb 
Date Detail:
Created Date:  2013-02-25     Completed Date:  2013-08-19     Revised Date:  2014-02-24    
Medline Journal Info:
Nlm Unique ID:  101230060     Medline TA:  J Chem Inf Model     Country:  United States    
Other Details:
Languages:  eng     Pagination:  384-90     Citation Subset:  IM    
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Bacteroides / enzymology*
Databases, Protein
Drug Design
Enzyme Inhibitors / chemistry,  pharmacology
Hepacivirus / enzymology*
Ligands
Molecular Docking Simulation / methods*
Probability
Protein Binding
RNA Replicase / antagonists & inhibitors*,  metabolism
Software
beta-N-Acetylhexosaminidases / antagonists & inhibitors*,  metabolism
Grant Support
ID/Acronym/Agency:
092076//Wellcome Trust
Chemical
Reg. No./Substance:
0/Enzyme Inhibitors; 0/Ligands; EC 2.7.7.48/RNA Replicase; EC 3.2.1.50/hexosaminidase C; EC 3.2.1.52/beta-N-Acetylhexosaminidases

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  Does arousal per se account for the influence of appetitive stimuli on attentional scope and the lat...
Next Document:  A conserved amphipathic ligand binding region influences k-path-dependent activity of cytochrome C o...