Document Detail


Multiple structures for Virtual Ligand Screening: defining binding site properties-based criteria to optimize the selection of the query.
MedLine Citation:
PMID:  23312043     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
Structure Based Virtual Ligand Screening (SBVLS) methods are widely used in drug discovery programs. When several structures of the target are available, protocols based either on single structure docking or on ensemble docking can be used. The performance of the methods depends on the structure(s) used as a reference, whose choice requires retrospective enrichment studies on benchmarking databases which consume additional resources. In the present study, we have identified several trends in the properties of the binding sites of the structures that led to the optimal performance in retrospective SBVLS tests whatever the docking program used (Surflex-dock or ICM). By assessing their hydrophobicity and comparing their volume and opening, we show that the selection of optimal structures should be possible with no requirement of prior retrospective enrichment studies. If the mean binding site volume is lower than 350A3, the structure with the smaller volume should be preferred. In the other cases, the structure with the largest binding site should be preferred. These optimal structures may be either selected for a single structure docking strategy or an ensemble docking strategy. When constructing an ensemble, the opening of the site might be an interesting criterion additionaly to its volume as the most closed structures should not be preferred in the large systems. These "binding-site-properties-based" guidelines could be helpful to optimize future prospective drug discovery protocols when several structures of the target are available.
Authors:
Nesrine Ben Nasr; Hélène Guillemain; Nathalie Lagarde; Jean-François Zagury; Matthieu Montes
Related Documents :
3132093 - Inhibition of tobramycin diffusion by binding to alginate.
23166753 - An integrative computational framework based on a two-step random forest algorithm impr...
9233683 - The high-affinity quinacrine binding site is located at a non-annular lipid domain of t...
Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2013-1-14
Journal Detail:
Title:  Journal of chemical information and modeling     Volume:  -     ISSN:  1549-960X     ISO Abbreviation:  J Chem Inf Model     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2013-1-14     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101230060     Medline TA:  J Chem Inf Model     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:

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


Previous Document:  Genotypic differences among rice cultivars in lead accumulation and translocation and the relation w...
Next Document:  High-density lipoprotein subclasses and their relationship to cardiovascular disease.