Table 2.

List of popular docking software and associated specifications

Program	OSC	lFlex	pFlex	Parallel	Algorithm	SF	SF class	Owner
GOLD		√	SP, RTML, MRC	CG	GA	GOLD_Fitness, Chemscore,	Empirical	CCDC
						ASP	Knowledge-based
eHiTS		√	SP	CG, FG	Fragment	eHiTS SF	Knowledge-based	SimBioSys
Surflex		√	SP	CG, FG	Protomol	Surflex SF	Empirical	Tripos
Glide		√	SP, side-chain repackinga	CG	Energy funnel, MC	GlideScore	Empirical	Schrödinger
						Emodel	Empirical+Force field-based
LigandFit		√	SP	CG, FG	MC	LigScore1/2	Empirical	Accelry
FlexX		√	MRCb	CG	Fragment	FlexX score	Empirical	BioSolveIT
ICM		√	SP, MRC	CG	MC	ICM SF	Empirical	Molsoft
						ICM-PMF	Knowledge-based
Fred				CG	RB	Chemgauss3, Chemscore, OEChemscore	Empirical	OpenEye
						Zapbindc	Force field-based
AutoDock	√	√	RTML	FG	GA, SA	AD4	Empirical	Scripps
DOCK	√	√	Full-atom flexibility during AMBER score calculation	FG	Fragment	DOCK3.5 score, GB/SA score, PB/SA scorec, AMBER score	Force field-based	UCSF
RosettaLigand	√	√	Side-chain repacking	FG	MC	Rosetta energy function	Knowledge-based	University of Washington

OSC=open source code; lFlex=ligand flexibility; pFlex=protein flexibility; SP=soft potentials; RTML=rotamer libraries; MRC=multiple receptor conformers; CG=coarse-grained parallelization; FG=fine-grained parallelization; SF=scoring function; GA=genetic algorithm; RB=rigid-body docking; SA=simulated annealling; Fragment=fragment-based algorithm; MC=Monte Carlo energy minimization; GB/SA=Generalized Boltzmann Surface Area; PB/SA=Poisson-Boltzmann Surface Area;

^aPrime (Schrödinger) is needed for induced fit docking.

^bFlexE (Tripos) is needed for MRC sampling.

^cZap package (OpenEye) is needed for PB/SA calculation.