Table 1.
Popular and useful software used in the different steps involved in a virtual screening workflow. A more complete list can be found at http://www.click2drug.org/.
| Method | Software | Developer |
|---|---|---|
| Graphical user interface | Flare [14] | Cresset |
| Maestro [33] | Schrödinger, LLC | |
| VIDA [34] | OpenEye Scientific Software Inc. | |
| Decoy set preparation | DecoyFinder [35] | Cheminformatics and Nutrition Research Group (Universitat Rovira I Virgili) |
| Crystal structure validation | VHELIBS [21] | Cheminformatics and Nutrition Research Group (Universitat Rovira I Virgili) |
| Molecule standardization | Standardizer [30] | ChemAxon |
| LigPrep [31] | Schrödinger, LLC | |
| MolVS [32] | RDKit | |
| Conformer generation | OMEGA [25] | OpenEye Scientific Software Inc. |
| ConfGen [26] | Schrödinger, LLC | |
| Distance Geometry (DG) [27] | RDKit | |
| ETKDG [29] | RDKit | |
| ADME property prediction | QikProp [36] | Schrödinger, LLC |
| SwissADME [37] | Swiss Institute of Bioinformatics | |
| FAFDrugs4 [38] | UMRS Paris Diderot-Inserm 973 | |
| Shape similarity | ROCS [39] | OpenEye Scientific Software Inc. |
| Shape screening [40] | Schrödinger, LLC | |
| Electrostatic potential similarity | EON [41] | OpenEye Scientific Software Inc. |
| Pharmacophore | Phase [42] | Schrödinger, LLC |
| Ligandscout [43] | Inte:Ligand GmbH | |
| Docking | Glide [44] | Schrödinger, LLC |
| GOLD [45] | The Cambridge Crystallographic Data Centre | |
| DOCK [46] | University of California San Francisco | |
| Autodock [47] | The Scripps Research Institute |