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

@article{CrossTRBFHH09, abstract = {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.}, author = {Cross, Jason B. and Thompson, David C. and Rai, Brajesh K. and Baber, J. Christian and Fan, Kristi Y. and Hu, Yongbo and Humblet, Christine}, citeulike-article-id = {4747005}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/ci900056c}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ci900056c}, day = {22}, doi = {10.1021/ci900056c}, journal = {Journal of Chemical Information and Modeling}, keywords = {accuracy, auc, based, binding, complexes, dock, docking, dud, effect, expert, families, flexx, glide, icm, knowledge, ligand, metric, modeling, modes, molecular, parameter, phdock, poses, predicting, protein, roc, screening, significant, structure, surflex, virtual, x-ray}, month = {June}, number = {6}, pages = {1455--1474}, posted-at = {2009-07-23 12:47:08}, priority = {2}, title = {Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy}, url = {http://dx.doi.org/10.1021/ci900056c}, volume = {49}, year = {2009} }

TY - JOUR ID - CrossTRBFHH09 L3 - citeulike-article-id:4747005 N2 - 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. IS - 6 JF - Journal of Chemical Information and Modeling EP - 1474 TI - Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy VL - 49 SP - 1455 KW - accuracy KW - auc KW - based KW - binding KW - complexes KW - dock KW - docking KW - dud KW - effect KW - expert KW - families KW - flexx KW - glide KW - icm KW - knowledge KW - ligand KW - metric KW - modeling KW - modes KW - molecular KW - parameter KW - phdock KW - poses KW - predicting KW - protein KW - roc KW - screening KW - significant KW - structure KW - surflex KW - virtual KW - x-ray AU - Cross, Jason AU - Thompson, David AU - Rai, Brajesh AU - Baber, Christian AU - Fan, Kristi AU - Hu, Yongbo AU - Humblet, Christine PY - 2009/06/22/ UR - http://dx.doi.org/10.1021/ci900056c ER -