… of three popular docking programs, Autodock, Autodock Vina, and Surflex-Dock for a series
of … Semi-flexible docking allows the ligands to sample various conformations during a semi-…

… because AutoDock … the ligands for flexible docking of macrocyclic structures, which is now
enabled by default in Meeko (Meeko, nd), our recently developed interface between AutoDock …

… to solve the flexible docking problem, such as Autodock [5], [6], Autodock Vina (referred to
… Our future work is to modify the scoring function of Autodock to make it more suitable for …

… Automated protein-ligand docking methods are effective … –ligand docking is flexible ligand
docking, in which ligands are … for flexible ligand docking based on the Autodock docking …

… MRMC approach with Autodock smina [Citation112]. They noted significantly lower total
energies and stronger interactions between protein and ligand when protein flexibility is added, …

… AutoDock is an open-source and automated docking package introduced by the Molecular
Graphics Lab, Scripps Research Institute, La Jolla, CA 92037, USA. It is effectively applied to …

… In standard protein–ligand docking, AutoDock-GPU uses an internal semiempirical force
field to estimate the binding energy between the ligand and protein. This accounts for six …

… and dimensions: a) “Automatic” - the program uses AutoLigand to predict possible binding
… We find the off-target docking procedure particularly helpful for conducting ligand selectivity …

… algorithms in Autodock, regardless of whether the flexible ligand docking problem has a …
of the search algorithms used in the Autodock software for flexible ligand docking, in this paper, …

… of ligand orientational/conformational sampling, which improves the accuracy of docking larger
and more flexible ligands… It is noted that AutoDock almost failed in flexible-ligand docking, …