A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

By E. Perola, W. Patrick Walters, P. Charifson. Proteins: Structure, Function, and Bioinformatics, 2004

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Advances and Challenges in Protein-Ligand Docking (2010, background): “Although many comparison studies for docking and scoring have been published [158–166], publicly available docking benchmarks such as DUD (http://dud.”
Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement (2012, unknown): “The ability of the algorithms to identify ligand-binding pocket is tested on 501 benchmarking proteins, collected from three previous experiments (Dessailly et al., 2008; Hartshorn et al., 2007; Perola et al., 2004), which harbor 582 ligands.”
ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility (2006, unknown): “5,11 Rather, the exact prediction of the protein conformation when binding the ligand was the objective of this work.”
Molecular docking: a powerful approach for structure-based drug discovery. (2011, methodology): “Considering the limitation of computer resources, docking has been performed with a flexible ligand and a rigid receptor for a long time, and remains the most popular method in use [7, 30-35].”
Computer-based de novo design of drug-like molecules (2005, background): “Consideration of automatically docked molecules would further extend the numbers of ideas generated by this algorith”