Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment

By Marcel L. Verdonk, V. Berdini, M. Hartshorn, Wijnand T. M. Mooij, Christopher W. Murray, Richard D. Taylor, P. Watson. Journal of Chemical Information and Modeling, 2004

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Comparing protein–ligand docking programs is difficult (2005, background): “A final point is that apparent enrichments may be trivial anyway; for example, they may merely reflect the fact that scoring functions are usually correlated with molecular size.(28) The key question is whether the observed enrichment could have been obtained without docking.”
What do we know and when do we know it? (2008, background): “The rationale is utilitarian; why should one chose to use sophisticated methods when simple, ligand-based, ones can do just as well? Approaches include matching physical properties, for instance size, number of hydrogen bond donors and acceptors, lipophilicity, charge or flexibility [ 17 ].”
Key Topics in Molecular Docking for Drug Design (2019, methodology): “Since information on inactive molecules is scarce in comparison to active ones, most decoys are not selected based on experimental data but are instead putative inactive compounds [85], whose selection must be made carefully so as to avoid artificial enrichment [86].”
Virtual ligand screening: strategies, perspectives and limitations (2006, methodology): “However, the choice of the random compound library is crucial and can strongly affect the enrichments obtained [72] .”