Ligand docking referred to cases where small molecule (“ligand”) is being docked into much larger macromolecule ("target"). The following is partial list of docking software, focusing on free (at least for academic institutes) and/or popular docking tools.
Stochastic (GA)
Flexible ligand and partially flexible target
Systematic
Flexible ligandX-Score based
Systematic (IC)
Flexible ligandDOCK 3.5 (force field)
Systematic (RBD of fragments followed by reconstruction)Flexible ligand and partially flexible targetHiTS_Score (empirical)
Systematic (IC)Flexible ligandFlexX SF (empirical)Commercial
Stochastic (GA)Flexible ligand and flexible targetAUTODOCK (empirical)
Systematic (RBD)Flexible ligandChemScore, PLP, ScreenScore, ChemGauss (empirical/consensus)
Stochastic (GA)
Flexible ligand and partially flexible targetGoldScore, ChemScore (empirical), ASP (knowledge based)
Stochastic (MC)
Flexible ligand and partially flexible targetICM SF (empirical)
Stochastic (MC)
RigidBAPPL (empirical)
Stochastic (ACO)Flexible ligand and partially flexible target
CHEMPLP, PLP (empirical)
Systematic (IC/MA)Flexible ligandHammerhead based (empirical)
Point to note:
Several studies have shown that the performance of most docking tools is highly dependent on the particular characteristics of both the binding site and the ligand to be investigated, and the determination which method would be more suitable in a specific context is difficult. We encouraged you to check several docking methods to determine which one(s) work best for your system.
