Comparison of shape-matching and docking as virtual screening tools.

By P. Hawkins, A. Skillman, Anthony Nicholls. 2007

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PotentialNet for Molecular Property Prediction (2018, background): “Cheminformatic featurizations include Extended Circular Fingerprints (ECFP) 12 and ROCS 13,14 .”
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking (2012, methodology): “48 Ligand sets from each species were combined, sorted by ascending normalized a ﬃ nity, and then made unique based on canonical smiles.”
Pharmit: interactive exploration of chemical space (2016, methodology): “A shape-first search with pharmacophore restraints is distinct from the commonly used ROCS with color shape method (25) as it does not optimize the position with respect to the pharmacophores.”
Visualisation and subsets of the chemical universe database GDB-13 for virtual screening (2011, methodology): “This 3D shape-based approach is well-validated for ligand-based virtual screening [ 36 ].”
Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations (2015, positive): “In fact, OpenEye recently developed a newer implementation (“FastROCS”) that takes advantage of multiple CPU and GPU cores, and is even faster than ROCS (163, 181).”