Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?

Journal of Computer-aided Molecular Design
Andrew C Good, T I Oprea

Abstract

Over the last few years many articles have been published in an attempt to provide performance benchmarks for virtual screening tools. While this research has imparted useful insights, the myriad variables controlling said studies place significant limits on results interpretability. Here we investigate the effects of these variables, including analysis of calculation setup variation, the effect of target choice, active/decoy set selection (with particular emphasis on the effect of analogue bias) and enrichment data interpretation. In addition the optimization of the publicly available DUD benchmark sets through analogue bias removal is discussed, as is their augmentation through the addition of large diverse data sets collated using WOMBAT.

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Citations

Feb 8, 2008·Journal of Computer-aided Molecular Design·Robert D Clark, Daniel J Webster-Clark
Feb 15, 2008·Journal of Computer-aided Molecular Design·John J Irwin
Mar 14, 2008·Journal of Computer-aided Molecular Design·Ajay N Jain, Anthony Nicholls
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Nov 6, 2010·Journal of Computer-aided Molecular Design·Natasja BrooijmansChristine Humblet
Nov 15, 2011·Journal of Computer-aided Molecular Design·Orr RavitzAniko Simon
Dec 29, 2011·Journal of Computer-aided Molecular Design·Nadine SchneiderMatthias Rarey
May 10, 2012·Journal of Computer-aided Molecular Design·Marco A C NevesRuben Abagyan
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