Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?
- 9 January 2008
- journal article
- research article
- Published by Springer Nature in Journal of Computer-Aided Molecular Design
- Vol. 22 (3-4) , 169-178
- https://doi.org/10.1007/s10822-007-9167-2
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.Keywords
This publication has 35 references indexed in Scilit:
- Benchmarking Sets for Molecular DockingJournal of Medicinal Chemistry, 2006
- Comparison of Automated Docking Programs as Virtual Screening ToolsJournal of Medicinal Chemistry, 2005
- Virtual screening of chemical librariesNature, 2004
- Successful Virtual Screening for a Submicromolar Antagonist of the Neurokinin-1 Receptor Based on a Ligand-Supported Homology ModelJournal of Medicinal Chemistry, 2004
- Influenza Virus Neuraminidase Inhibitors: Generation and Comparison of Structure-Based and Common Feature Pharmacophore Hypotheses and Their Application in Virtual ScreeningJournal of Chemical Information and Computer Sciences, 2004
- Target-biased scoring approaches and expert systems in structure-based virtual screeningCurrent Opinion in Chemical Biology, 2004
- Virtual Screening for Submicromolar Leads of tRNA-guanine Transglycosylase Based on a New Unexpected Binding Mode Detected by Crystal Structure AnalysisJournal of Medicinal Chemistry, 2003
- Similarity Searching Using Reduced GraphsJournal of Chemical Information and Computer Sciences, 2003
- From atoms and bonds to three-dimensional atomic coordinates: automatic model buildersChemical Reviews, 1993
- Substructure searching methods: Old and newJournal of Chemical Information and Computer Sciences, 1993