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Table 2 Surveyed tools for the analysis of docking simulations and protein-ligand complexes (presented in alphabetical order)

From: Survey of public domain software for docking simulations and virtual screening

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