List of protein-ligand docking software

The number of protein-ligand docking programs currently available is high and has been steadily increasing over the last decades. The following list presents an overview of the most common programs, listed alphabetically, with indication of the corresponding year of publication, involved organisation or institution, short description, availability of a webservice and the license. This table is comprehensive but not complete.a

Program	Year Published	Organisation	Description	Webservice	License
1-Click Docking	2011	Mcule	Docking predicts the binding orientation and affinity of a ligand to a target	Yes	Free to use webservice
AADS	2011	Indian Institute of Technology	Automated active site detection, docking, and scoring(AADS) protocol for proteins with known structures based on Monte Carlo Method	Yes	Free to use webservice
ADAM	1994	IMMD Inc.	Prediction of stable binding mode of flexible ligand molecule to target macromolecule	No	Commercial
AutoDock	1990	The Scripps Research Institute	Automated docking of ligand to macromolecule by Lamarckian Genetic Algorithm and Empirical Free Energy Scoring Function	No	Open source (GNU GPL)
AutoDock Vina	2010	The Scripps Research Institute	New generation of AutoDock	No	Open source (Apache License)
AutoDock Vina Extended	2018	OneAngstrom	Extension of AutoDock Vina for easy setup and analysis	No	Commercial
BetaDock	2011	Hanyang University	Based on Voroni Diagram	No	Freeware
Blaster	2009	University of California San Francisco	Combines ZINC databases with DOCK to find ligand for target protein	Available	Freeware
BSP-SLIM	2012	University of Michigan	A new method for ligand-protein blind docking using low-resolution protein structures	Available	Freeware
CABS-dock	2015	University of Warsaw	A method for flexible protein-peptide docking without a priori knowledge about the binding site. Available as a standalone application[1] and as a web server.[2]	Available	Open source (MIT License) (standalone application) Freeware for academic use (web server)
DARWIN	2000	The Wistar Institute	Prediction of the interaction between a protein and another biological molecule by genetic algorithm	No	Freeware
DIVALI	1995	University of California-San Francisco	Based on AMBER-type potential function and genetic algorithm	No	Freeware
DOCK	1988	University of California-San Francisco	Based on Geometric Matching Algorithm	No	Freeware for academic use
DockingServer	2009	Virtua Drug Ltd	Integrates a number of computational chemistry software	Yes	Commercial
Docking Study with HyperChem	2006	Motonori Tsuji	Biomacromolecule- and ligand-flexible docking using combination between the predicted structure-based pharmacophores and ligand-based pharmacophores	No	Commercial
DockVision	1992	DockVision	Based on Monte Carlo, genetic algorithm, and database screening docking algorithms	No	Commercial
DOLINA	2014	University of Basel	Pharmacophore-based alignment, local combinatorial induced-fit	No	Academic
EADock[3]	2007	Swiss Institute of Bioinformatics	Based on evolutionary algorithms	Available	Freeware
eHiTS	2006	SymBioSys Inc	Exhausted search algorithm	No	Commercial
EUDOC	2001	Mayo Clinic Cancer Center	Program for identification of drug interaction sites in macromolecules and drug leads from chemical databases	No	Academic
FDS	2003	University of Southampton	Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function	No	Academic
Fitted	2010	Molecular Forecaster Inc.	Docking program with flexibility, covalent, metalloenzyme, displaceable water considerations	No	Freeware for academic use
FlexX	2001	BioSolveIT	Incremental build based docking program	No	Commercial
FlexAID	2015	University of Sherbrooke	Target side-chain flexibility and soft scoring function, based on surface complementarity	No	Open source (Apache License)
FlexPepDock	2010	The Hebrew University	Modeling of peptide-protein complexes, implemented within the Rosetta framework	Available	Freeware
FLIPDock	2007	Scripps Research Institute	Genetic algorithm based docking program using FlexTree data structures to represent a protein-ligand complex	No	Freeware for academic use
FLOG	1994	Merck Research Laboratories	Rigid body docking program using databases of pregenerated conformations	No	Academic
FRED	2003	OpenEye Scientific	Systematic, exhaustive, nonstochastic examination of all possible poses within the protein active site combined with scoring Function	No	Freeware for academic use
FTDOCK	1997	Biomolecular Modelling Laboratory	Based on Katchalski-Katzir algorithm. It discretises the two molecules onto orthogonal grids and performs a global scan of translational and rotational space	No	Freeware
GalaxyPepDock	2018	Seoul National University	Protein-peptide docking based on interaction similarity available as a standalone application[4] and a web server[5]	Available	Open source (GNU GPL) (standalone application) Freeware for academic use (web server)
GEMDOCK	2004	National Chiao Tung University	Generic Evolutionary Method for molecular docking	No	Freeware
Glide	2004	Schrödinger	Exhaustive search based docking program	No	Commercial
GOLD	1995	Collaboration between the University of Sheffield, GlaxoSmithKline plc and CCDC	Genetic algorithm based, flexible ligand, partial flexibility for protein	No	Commercial
GPCRautomodel	2012	INRA	Automates the homology modeling of mammalian olfactory receptors (ORs) based on the six three-dimensional (3D) structures of G protein-coupled receptors (GPCRs) available so far and performs the docking of odorants on these models	Available	Freeware for academic use
HADDOCK	2003	Centre Bijvoet Center for Biomolecular Research	Makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions. Developed for protein-protein docking, but can also be applied to protein-ligand docking.	Available	Academic[6] Free to use webservice available
Hammerhead	1996	Arris Pharmaceutical Corporation	Fast, fully automated docking of flexible ligands to protein binding sites	No	Academic
ICM-Dock	1997	MolSoft	Docking program based on pseudo-Brownian sampling and local minimization	No	Commercial
idTarget	2012	National Taiwan University	Predicts possible binding targets of a small chemical molecule via a divide-and-conquer docking approach	Available	Freeware
iScreen	2011	China Medical University	Based on a cloud-computing system for TCM intelligent screening system	Available	Freeware
Lead finder	2008	MolTech	Program for molecular docking, virtual screening and quantitative evaluation of ligand binding and biological activity	No	Commercial
LeDock	2016	Lephar	Program for fast and accurate flexible docking of small molecules into a protein	No	Freeware for academic use
LigandFit	2003	BioVia	CHARMm based docking program	No	Commercial
LigDockCSA	2011	Seoul National University	Protein-ligand docking using conformational space annealing	No	Academic
LightDock[7]	2018	Barcelona Supercomputing Center	Protein-protein, protein-DNA, protein-peptide docking using different scoring functions, backbone flexibility modeled by ANM and written in Python3	No	Open source (GNU GPL)
LIGIN	1996	Weizmann Institute of Science	Molecular docking using surface complementarity	No	Commercial
LPCCSU	1999	Weizmann Institute of Science	Based on a detailed analysis of interatomic contacts and interface complementarity	Available	Freeware
MCDOCK	1999	Georgetown University Medical Center	Based on a non-conventional Monte Carlo simulation technique	No	Academic
MEDock	2007	SIGMBI	Maximum-Entropy based Docking web server is aimed at providing an efficient utility for prediction of ligand binding site	Available	Freeware
MedusaDock	2010	Dokholyan Laboratory	Rapid flexible docking using a stochastic rotamer library of ligands.	Yes	Free to use
Molecular Operating Environment (MOE)	2008	Chemical Computing Group	Docking application within MOE; choice of placement methods (including alpha sphere methods) and scoring functions (including London dG)	No	Commercial
Molegro Virtual Docker	2006	Molexus	Based on a new heuristic search algorithm that combines differential evolution with a cavity prediction algorithm	No	Academic
MOLS 2.0	2016	University of Madras	Induced-fit peptide-protein, small molecule-protein docking using mutually orthogonal Latin squares technique	No	Open source (GNU LGPL)
MS-DOCK	2008	INSERM	Multi-stage docking/scoring protocol	No	Academic Commercial
ParaDockS[8]	2010	Martin Luther University of Halle-Wittenberg and Partner Institute for Computational Biology	Molecular docking with population-based metaheuristics	No	Open source (GNU GPL)
ParDOCK	2007	Indian Institute of Technology	All-atom energy based Monte Carlo, rigid protein ligand docking	Available	Freeware
PatchDock	2002	Tel Aviv University	The algorithm carries out rigid docking, with surface variability/flexibility implicitly addressed through liberal intermolecular penetration	Available	Freeware
PLANTS	2006	University of Konstanz	Based on a class of stochastic optimization algorithms (ant colony optimization)	No	Freeware for academic use
PLATINUM	2008	Moscow Institute of Physics and Technology (State University)	Analysis and visualization of hydrophobic/hydrophilic properties of biomolecules supplied as 3D-structures	Available	Freeware
PRODOCK	1999	Cornell University	Based on Monte Carlo method plus energy minimization	No	Academic
PSI-DOCK[9]	2006	Peking University	Pose-Sensitive Inclined (PSI)-DOCK	No	Academic
PSO@AUTODOCK	2007	University of Leipzig	Particle Swarm Optimization (PSO) algorithms varCPSO and varCPSO-ls are suited for rapid docking of highly flexible ligands	No	Academic
PythDock	2011	Hanyang University	Heuristic docking program that uses Python programming language with a simple scoring function and a population based search engine	No	Academic
Q-Dock	2008	Georgia Institute of Technology	Low-resolution flexible ligand docking with pocket-specific threading restraints	No	Freeware
QXP[10]	1997	Novartis Pharmaceuticals Corporation	Monte Carlo perturbation with energy minimization in Cartesian space	No	Academic
rDock	1998 (commercial) 2006 (academic)[11] 2012 (open source)[12]	Vernalis R&D (commercial) University of York (academic) University of Barcelona (open source)	HTVS of small molecules against proteins and nucleic acids, binding mode prediction	No	Open source (GNU LGPL) (formerly commercial, academic)
SANDOCK	1998	University of Edinburgh	Guided matching algorithm	No	Academic
Score	2004	Alessandro Pedretti & Giulio Vistoli	The Score service allows to calculate some different docking scores of ligand-receptor complex	Available	Freeware
SEED	1999	University of Zurich	Automated docking of fragments with evaluation of free energy of binding including electrostatic solvation effects in the continuum dielectric approximation (generalized Born)	No	Open source (GNU GPL)
smina	2012	University of Pittsburgh	A customized fork of AutoDock Vina with a better support scoring function and a high-performance energy minimization	No	Open source (Apache License)
SODOCK	2007	Feng Chia University (Taiwan)	Swarm optimization for highly flexible protein-ligand docking	No	Academic
SOFTDocking	1991	University of California, Berkeley	Matching of molecular surface cubes	No	Academic
Surflex-Dock	2003	Tripos	Based on an idealized active site ligand (a protomol)	No	Commercial
SwissDock	2011	Swiss Institute of Bioinformatics	Webservice to predict interaction between a protein and a small molecule ligand	Available	Free to use webservice for academic usage
VoteDock	2011	University of Warsaw	Consensus docking method for prediction of protein-ligand interactions	No	Academic
YUCCA	2005	Virginia Tech	Rigid protein-small-molecule docking	No	Academic

References

1. "CABSdock standalone application for protein-peptide docking". bitbucket.org. Retrieved 2019-05-22.
2. "CABS-dock: server for protein-peptide docking". biocomp.chem.uw.edu.pl. Retrieved 2019-05-22.
3. Grosdidier, Aurélien; Zoete, Vincent; Michielin, Olivier (2007). "EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization". Proteins: Structure, Function, and Bioinformatics. 67 (4): 1010–1025. doi:10.1002/prot.21367. ISSN 1097-0134. PMID 17380512. S2CID 11145933.
4. "GalaxyPepDock". GalaxyPepDock. Retrieved 2019-05-22.
5. "GalaxyWEB". galaxy.seoklab.org. Retrieved 2019-05-22.
6. "HADDOCK2.2 licensing". Bonvin Lab. Retrieved 2019-05-24.
7. Jimenez-Garcia, Brian (2019-09-28), Protein docking framework based on the GSO algorithm: lightdock/lightdock, retrieved 2019-09-28
8. Baldauf, Carsten (2017-08-22), Framework for molecular docking with population-based metaheuristics: cbaldauf/paradocks, retrieved 2019-06-01
9. Pei, Jianfeng; Wang, Qi; Liu, Zhenming; Li, Qingliang; Yang, Kun; Lai, Luhua (2006-03-01). "PSI-DOCK: towards highly efficient and accurate flexible ligand docking". Proteins. 62 (4): 934–946. doi:10.1002/prot.20790. ISSN 1097-0134. PMID 16395666. S2CID 5715684.
10. McMartin, C.; Bohacek, R. S. (July 1997). "QXP: powerful, rapid computer algorithms for structure-based drug design". Journal of Computer-Aided Molecular Design. 11 (4): 333–344. Bibcode:1997JCAMD..11..333M. doi:10.1023/a:1007907728892. ISSN 0920-654X. PMID 9334900. S2CID 31660790.
11. "rDock". www.ysbl.york.ac.uk. Retrieved 2020-02-12.
12. "About | rDock". Retrieved 2020-02-12.

External links

• "Protein-ligand docking bioinformatics tools | Interaction analysis". omicX. Retrieved 2019-05-23.