EasyDock: customizable and scalable docking tool

Table 4 The list of freely available automated docking protocols

Program name	Year	Supported docking programs	Input	Protonation	3D embedding	Stereoisomers/ tautomers	Parallel computing	Ref	Repository link
Vina MPI	2013	vina	pdbqt				MPI	[11]
VirtualFlow	2020	vina qvina qvina-w vina-carb smina autodockFR		cxcalc	chemaxon openbabel	A major tautomer (cxcalc)	SLURM Moab TORQUE PBS	[6]	https://github.com/VirtualFlow/VFVS
DockStream	2021	vina glide gold hybrid rDock		epik	corina ligprep omega rdkit	Enumeration of tautomers and stereoisomers	Across cores	[12]	https://github.com/MolecularAI/DockStream
DOCK	2021	DOCK	3D molecules				SGE PBS SLURM	[13]
DockString	2022	vina	SMILES	openbabel, pH = 7.4	rdkit	Consistent random stereoisomer (rdkit)	A single mol dock can use multiple cores	[15]	https://github.com/dockstring/dockstring
ChemFlow	2023	plants vina qvina smina	SMILES, 2D SDF	epic	cxcalc	Dominant tautomers (> 10% probability), enumerate stereoisomers (cxcalc)	PBS SLURM	[14]	https://github.com/IFMlab/ChemFlow
EasyDock	2023	vina gnina smina	SMILES, 2D/3D SDF	cxcalc, pH = 7.4 (optional)	rdkit if input is not 3D	A major tautomer (cxcalc, optional) consistent random stereoisomer (rdkit)	Across cores and network nodes (Dask)	This work	https://github.com/ci-lab-cz/easydock

ISSN: 1758-2946