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J Chem Inf Model. 2011 Jun 27;51(6):1439-46. doi: 10.1021/ci200117n. Epub 2011 May 12.

Predictive power of molecular dynamics receptor structures in virtual screening.

Author information

1
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0365, United States. senichols@ucsd.edu

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.

PMID:
21534609
PMCID:
PMC3124922
DOI:
10.1021/ci200117n
[Indexed for MEDLINE]
Free PMC Article
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