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Predictive power of molecular dynamics receptor structures in virtual screening.
- 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.
- Subjects :
- Cytochrome-c Peroxidase genetics
Cytochrome-c Peroxidase metabolism
HIV Reverse Transcriptase antagonists & inhibitors
HIV Reverse Transcriptase chemistry
HIV Reverse Transcriptase metabolism
HIV-1 enzymology
Protein Conformation
Proteins chemistry
ROC Curve
Reverse Transcriptase Inhibitors pharmacology
Drug Evaluation, Preclinical methods
Molecular Dynamics Simulation
Proteins metabolism
User-Computer Interface
Subjects
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