Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?

By Johannes Kirchmair, P. Markt, S. Distinto, Gerhard Wolber, T. Langer. 2008

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Molecular Docking and Structure-Based Drug Design Strategies (2015, background): “Conformational changes, resulting from interaction with ligands, and structural resolution are important details requiring consideration in the selection of the most suitable structure [170,171].”
Challenges and advances in computational docking: 2009 in review (2011, background): “Cross and co-workers have investigated the effect of input conformation (crystal vs. CORINA-generated structures, advocated by Kirchmair et al ., (46)) on the accuracy of pose prediction (47).”
Key Topics in Molecular Docking for Drug Design (2019, background): “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].”