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FRED Pose Prediction and Virtual Screening Accuracy

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Cite this: J. Chem. Inf. Model. 2011, 51, 3, 578–596
Publication Date (Web):February 16, 2011
https://doi.org/10.1021/ci100436p
Copyright © 2011 American Chemical Society

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    Abstract

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    Results of a previous docking study are reanalyzed and extended to include results from the docking program FRED and a detailed statistical analysis of both structure reproduction and virtual screening results. FRED is run both in a traditional docking mode and in a hybrid mode that makes use of the structure of a bound ligand in addition to the protein structure to screen molecules. This analysis shows that most docking programs are effective overall but highly inconsistent, tending to do well on one system and poorly on the next. Comparing methods, the difference in mean performance on DUD is found to be statistically significant (95% confidence) 61% of the time when using a global enrichment metric (AUC). Early enrichment metrics are found to have relatively poor statistical power, with 0.5% early enrichment only able to distinguish methods to 95% confidence 14% of the time.

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    A complete set of figures and tables for early enrichment results, a list of the OMEGA and FRED options used for each mode, and more. This material is available free of charge via the Internet at http://pubs.acs.org.

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