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Predictive power of molecular dynamics receptor structures in virtual screening.

Authors :
Nichols SE
Baron R
Ivetac A
McCammon JA
Source :
Journal of chemical information and modeling [J Chem Inf Model] 2011 Jun 27; Vol. 51 (6), pp. 1439-46. Date of Electronic Publication: 2011 May 12.
Publication Year :
2011

Abstract

Molecular dynamics (MD) simulation is a well-established method for understanding protein dynamics. Conformations from unrestrained MD simulations have yet to be assessed for blind virtual screening (VS) by docking. This study presents a critical analysis of the predictive power of MD snapshots to this regard, evaluating two well-characterized systems of varying flexibility in ligand-bound and unbound configurations. Results from such VS predictions are discussed with respect to experimentally determined structures. In all cases, MD simulations provide snapshots that improve VS predictive power over known crystal structures, possibly due to sampling more relevant receptor conformations. Additionally, MD can move conformations previously not amenable to docking into the predictive range.

Details

Language :
English
ISSN :
1549-960X
Volume :
51
Issue :
6
Database :
MEDLINE
Journal :
Journal of chemical information and modeling
Publication Type :
Academic Journal
Accession number :
21534609
Full Text :
https://doi.org/10.1021/ci200117n