Table 2.

List of some commonly used molecular dynamics and docking software packages with developer URL. This is not intended to be a comprehensive list of all available dynamics and docking programs available. Available programs are typically free to download for academic use, but some require the purchase of a license for use.

Dynamics		Docking
Program	Developer Site	Program	Developer site
Amber	http://ambermd.org/	AutoDock	http://autodock.scripps.edu/
AMMP	http://www.cs.gsu.edu/~cscrwh/progs/progs.html	FlexX	http://www.biosolveit.de/FlexX/
BALLview	http://www.ballview.org/	FRED	http://www.eyesopen.com/
CHARMM	http://www.charmm.org/	GLIDE	http://www.schrodinger.com/
GROMACS	http://www.gromacs.org/	GOLD	http://www.ccdc.cam.ac.uk/
LOOS Library	http://membrane.urmc.rochester.edu/Software	Sculptor	http://sculptor.biomachina.org/
YASARA	http://www.yasara.org/	SLIDE	http://www.bch.msu.edu/
YUP	http://rumour.biology.gatech.edu/YammpWeb/	SURFLEX	http://www.tripos.com/
ZMM	http://www.zmmsoft.com/	UCSF DOCK	http://dock.compbio.ucsf.edu/