Table 2.
Surveyed tools for the analysis of docking simulations and protein-ligand complexes (presented in alphabetical order)
| Tool | Platform | Availability | Accepted formats | Primary application | Reference |
|---|---|---|---|---|---|
| AutoDockTools | Standalone: Windows, Linux, MacOS | Pre-compiled and source code Free for academic use | Proprietary (DLG) | AutoDock | 10 |
| URL | http://autodock.scripps.edu/resources/adt | ||||
| DockingServer Jmol- and VMD-based | Web-based, platform independent | Commercial product, limited free use | PDB | AutoDock | 36 |
| URL | http://www.dockingserver.com/web | ||||
| LIGPLOT | Stand alone: Windows, Linux | Pre-compiled Free for academic use | PDB, Proprietary (HHB, NNB) | PDB | 34 |
| URL | http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/ | ||||
| POLYVIEW-MM Jmol- and PyMol-based | Web-based, platform independent | Free for everyone | PDB, Proprietary (DLG) | Any ligand docking program with output in the PDB format | 38 |
| URL | http://polyview.cchmc.org/conform.html | ||||
| ViewDock, Chimera-based | Standalone: Windows, Linux, MacOS | Pre-compiled and source code Free for academic use | PDB, MOL2, Proprietary (MORDOR) | DOCK | 37 |
| URL | http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html | ||||
| vsLab, VMD-based | Standalone: Linux, MacOS | Source code Free for everyone | PDB, MOL2 | AutoDock | 35 |
| URL | http://www.fc.up.pt/pessoas/nscerque/vsLab/vLab/HomePage.html | ||||