Table 4.
Software of interest for computer-aided drug discovery
| Software | Free license | Capabilities | Web-link | Reference |
|---|---|---|---|---|
| SwissDock | Yes | Molecular docking with rigid target | http://www.swissdock.ch/ | Grosdidier et al. (2011) |
| AutoDock 4 | Yes | Molecular docking with rigid target or allowing flexible residues | http://autodock.scripps.edu/ | Morris et al. (2009) |
| AutoDock Vina | Yes | Rigid docking, online server | http://vina.scripps.edu/ | Trott and Olson (2010) |
| ZDOCK | Yes | https://zlab.umassmed.edu/zdock/ | Pierce et al. (2011) | |
| OEDocking | Trial | Molecular docking, flexible fitting, 2D and 3D similarity | https://www.eyesopen.com/oedocking | Kelley et al. (2015) |
| DOCK | Yes | Molecular docking with rigid target | http://dock.compbio.ucsf.edu/ | Allen et al. (2015) |
| GOLD | No | Molecular docking with rigid target, side-chain flexibility, and ensemble docking | https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold/ | Jones et al. (1997) |
| Glide | No | Protein homology modelling | https://www.schrodinger.com/glide | Friesner et al. (2006) |
| FlexX | No | https://www.biosolveit.de/flexx/ | Rarey et al. (1996) | |
| SwissModel | Yes | https://swissmodel.expasy.org/ | Waterhouse et al. (2018) | |
| I-TASSER | Yes | Setting of docking parameters, docking results and molecular visualization | https://zhanglab.ccmb.med.umich.edu/I-TASSER/ | Yang and Zhang (2015) |
| Modeller | Yes | https://salilab.org/modeller/ | Webb and Sali (2016) | |
| AutoDock Tools | Yes | http://autodock.scripps.edu/ | Morris et al. (2009) | |
| Pymol | Yes | Molecular visualization | https://pymol.org/ | Schrödinger (USA) |
| VMD | Yes | Ligand and receptor-based pharmacophores | https://www.ks.uiuc.edu/Research/vmd/ | Humphrey et al. (1996) |
| Ligand Scout | Trial | http://www.inteligand.com/ligandscout/ | Wolber and Langer (2005) | |
| Discovery Studio | Visualizer only | Ligand and receptor-based pharmacophore, docking, ligand design, physico-chemical predictions, molecular graphics | https://www.3dsbiovia.com/ | Dassault Systèmes BIOVIA (2017) |
| Phase | No | Ligand and receptor-based pharmacophores, 3D QSAR | https://www.schrodinger.com/phase/ | Dixon et al. (2006) |
| LiSiCA | Yes | 2D and 3D similarity | http://insilab.org/lisica/ | Lesnik et al. (2015) |
| ShaEP | Yes | 3D small molecule alignment and similarity | http://users.abo.fi/mivainio/shaep/ | Vainio et al. (2009) |
| fPocket | Yes | Protein pocket prediction | http://fpocket.sourceforge.net/ | Schmidtke et al. (2010) |
| Gromacs | Yes | Molecular dynamics | http://www.gromacs.org/ | James Abraham et al. (2015) |
| AMBER suite | No | https://ambermd.org/ | Case et al. (2018) | |
| Dalton | Yes | Calculation of molecular descriptors 1D, 2D, and 3D | https://daltonprogram.org/ | Aidas et al. (2014) |
| PaDEL | Yes | http://www.yapcwsoft.com/dd/padeldescriptor/ | Yap (2011) |