Survey of public domain software for docking simulations and virtual screening

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

ISSN: 1479-7364