Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy

Molecular docking programs are widely used modeling tools for predicting ligand binding modes and structure based virtual screening. In this study, six molecular docking programs (DOCK, FlexX, GLIDE, ICM, PhDOCK, and Surflex) were evaluated using metrics intended to assess docking pose and virtual s...

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Bibliographic Details
Published in:Journal of Chemical Information and Modeling 2009-06, Vol.49 (6), p.1455-1474
Main Authors: Cross, Jason B, Thompson, David C, Rai, Brajesh K, Baber, J. Christian, Fan, Kristi Yi, Hu, Yongbo, Humblet, Christine
Format: Article
Language:English
Subjects:
Accuracy
Comparative analysis
Computational Chemistry
Crystallography, X-Ray
Drug Evaluation, Preclinical - methods
Ligands
Models, Molecular
Molecular Conformation
Molecules
Proteins
Proteins - chemistry
Proteins - metabolism
ROC Curve
Studies
User-Computer Interface
X-rays
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Summary:Molecular docking programs are widely used modeling tools for predicting ligand binding modes and structure based virtual screening. In this study, six molecular docking programs (DOCK, FlexX, GLIDE, ICM, PhDOCK, and Surflex) were evaluated using metrics intended to assess docking pose and virtual screening accuracy. Cognate ligand docking to 68 diverse, high-resolution X-ray complexes revealed that ICM, GLIDE, and Surflex generated ligand poses close to the X-ray conformation more often than the other docking programs. GLIDE and Surflex also outperformed the other docking programs when used for virtual screening, based on mean ROC AUC and ROC enrichment values obtained for the 40 protein targets in the Directory of Useful Decoys (DUD). Further analysis uncovered general trends in accuracy that are specific for particular protein families. Modifying basic parameters in the software was shown to have a significant effect on docking and virtual screening results, suggesting that expert knowledge is critical for optimizing the accuracy of these methods.
ISSN:1549-9596
1520-5142
1549-960X
DOI:10.1021/ci900056c