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

ProgramYear PublishedOrganisationDescriptionWebserviceLicense
1-Click Docking2011MculeDocking predicts the binding orientation and affinity of a ligand to a targetYesFree to use webservice
AADS2011Indian Institute of TechnologyAutomated active site detection, docking, and scoring(AADS) protocol for proteins with known structures based on Monte Carlo MethodYesFree to use webservice
ADAM1994IMMD Inc.Prediction of stable binding mode of flexible ligand molecule to target macromoleculeNoCommercial
AutoDock1990The Scripps Research InstituteAutomated docking of ligand to macromolecule by Lamarckian Genetic Algorithm and Empirical Free Energy Scoring FunctionNoOpen source (GNU GPL)
AutoDock Vina2010The Scripps Research InstituteNew generation of AutoDockNoOpen source (Apache License)
AutoDock Vina Extended2018OneAngstromExtension of AutoDock Vina for easy setup and analysisNoCommercial
BetaDock2011Hanyang UniversityBased on Voroni DiagramNoFreeware
Blaster2009University of California San FranciscoCombines ZINC databases with DOCK to find ligand for target proteinAvailableFreeware
BSP-SLIM2012University of MichiganA new method for ligand-protein blind docking using low-resolution protein structuresAvailableFreeware
CABS-dock2015University of WarsawA 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]AvailableOpen source (MIT License) (standalone application)
Freeware for academic use (web server)
DARWIN2000The Wistar InstitutePrediction of the interaction between a protein and another biological molecule by genetic algorithmNoFreeware
DIVALI1995University of California-San FranciscoBased on AMBER-type potential function and genetic algorithmNoFreeware
DOCK1988University of California-San FranciscoBased on Geometric Matching AlgorithmNoFreeware for academic use
DockingServer2009Virtua Drug LtdIntegrates a number of computational chemistry softwareYesCommercial
Docking Study with HyperChem2006Motonori TsujiBiomacromolecule- and ligand-flexible docking using combination between the predicted structure-based pharmacophores and ligand-based pharmacophoresNoCommercial
DockVision1992DockVisionBased on Monte Carlo, genetic algorithm, and database screening docking algorithmsNoCommercial
DOLINA2014University of BaselPharmacophore-based alignment, local combinatorial induced-fitNoAcademic
EADock[3]2007Swiss Institute of BioinformaticsBased on evolutionary algorithmsAvailableFreeware
eHiTS2006SymBioSys IncExhausted search algorithmNoCommercial
EUDOC2001Mayo Clinic Cancer CenterProgram for identification of drug interaction sites in macromolecules and drug leads from chemical databasesNoAcademic
FDS2003University of SouthamptonFlexible ligand and receptor docking with a continuum solvent model and soft-core energy functionNoAcademic
Fitted2010Molecular Forecaster Inc.Docking program with flexibility, covalent, metalloenzyme, displaceable water considerationsNoFreeware for academic use
FlexX2001BioSolveITIncremental build based docking programNoCommercial
FlexAID2015University of SherbrookeTarget side-chain flexibility and soft scoring function, based on surface complementarityNoOpen source (Apache License)
FlexPepDock2010The Hebrew UniversityModeling of peptide-protein complexes, implemented within the Rosetta frameworkAvailableFreeware
FLIPDock2007Scripps Research InstituteGenetic algorithm based docking program using FlexTree data structures to represent a protein-ligand complexNoFreeware for academic use
FLOG1994Merck Research LaboratoriesRigid body docking program using databases of pregenerated conformationsNoAcademic
FRED2003OpenEye ScientificSystematic, exhaustive, nonstochastic examination of all possible poses within the protein active site combined with scoring FunctionNoFreeware for academic use
FTDOCK1997Biomolecular Modelling LaboratoryBased on Katchalski-Katzir algorithm. It discretises the two molecules onto orthogonal grids and performs a global scan of translational and rotational spaceNoFreeware
GalaxyPepDock2018Seoul National UniversityProtein-peptide docking based on interaction similarity available as a standalone application[4] and a web server[5]AvailableOpen source (GNU GPL) (standalone application)
Freeware for academic use (web server)
GEMDOCK2004National Chiao Tung UniversityGeneric Evolutionary Method for molecular dockingNoFreeware
Glide2004SchrödingerExhaustive search based docking programNoCommercial
GOLD1995Collaboration between the University of Sheffield, GlaxoSmithKline plc and CCDCGenetic algorithm based, flexible ligand, partial flexibility for proteinNoCommercial
GPCRautomodel2012INRAAutomates 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 modelsAvailableFreeware for academic use
HADDOCK2003Centre Bijvoet Center for Biomolecular ResearchMakes 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.AvailableAcademic[6]
Free to use webservice available
Hammerhead1996Arris Pharmaceutical CorporationFast, fully automated docking of flexible ligands to protein binding sitesNoAcademic
ICM-Dock1997MolSoftDocking program based on pseudo-Brownian sampling and local minimizationNoCommercial
idTarget2012National Taiwan UniversityPredicts possible binding targets of a small chemical molecule via a divide-and-conquer docking approachAvailableFreeware
iScreen2011China Medical UniversityBased on a cloud-computing system for TCM intelligent screening systemAvailableFreeware
Lead finder2008MolTechProgram for molecular docking, virtual screening and quantitative evaluation of ligand binding and biological activityNoCommercial
LeDock2016LepharProgram for fast and accurate flexible docking of small molecules into a proteinNoFreeware for academic use
LigandFit2003BioViaCHARMm based docking programNoCommercial
LigDockCSA2011Seoul National UniversityProtein-ligand docking using conformational space annealingNoAcademic
LightDock[7]2018Barcelona Supercomputing CenterProtein-protein, protein-DNA, protein-peptide docking using different scoring functions, backbone flexibility modeled by ANM and written in Python3NoOpen source (GNU GPL)
LIGIN1996Weizmann Institute of ScienceMolecular docking using surface complementarityNoCommercial
LPCCSU1999Weizmann Institute of ScienceBased on a detailed analysis of interatomic contacts and interface complementarityAvailableFreeware
MCDOCK1999Georgetown University Medical CenterBased on a non-conventional Monte Carlo simulation techniqueNoAcademic
MEDock2007SIGMBIMaximum-Entropy based Docking web server is aimed at providing an efficient utility for prediction of ligand binding siteAvailableFreeware
MedusaDock 2010 Dokholyan Laboratory Rapid flexible docking using a stochastic rotamer library of ligands. Yes Free to use
Molecular Operating Environment (MOE)2008Chemical Computing GroupDocking application within MOE; choice of placement methods (including alpha sphere methods) and scoring functions (including London dG)NoCommercial
Molegro Virtual Docker2006MolexusBased on a new heuristic search algorithm that combines differential evolution with a cavity prediction algorithmNoAcademic
MOLS 2.02016University of MadrasInduced-fit peptide-protein, small molecule-protein docking using mutually orthogonal Latin squares techniqueNoOpen source (GNU LGPL)
MS-DOCK2008INSERMMulti-stage docking/scoring protocolNoAcademic
Commercial
ParaDockS[8]2010Martin Luther University of Halle-Wittenberg and Partner Institute for Computational BiologyMolecular docking with population-based metaheuristicsNoOpen source (GNU GPL)
ParDOCK2007Indian Institute of TechnologyAll-atom energy based Monte Carlo, rigid protein ligand dockingAvailableFreeware
PatchDock2002Tel Aviv UniversityThe algorithm carries out rigid docking, with surface variability/flexibility implicitly addressed through liberal intermolecular penetrationAvailableFreeware
PLANTS2006University of KonstanzBased on a class of stochastic optimization algorithms (ant colony optimization)NoFreeware for academic use
PLATINUM2008Moscow Institute of Physics and Technology (State University)Analysis and visualization of hydrophobic/hydrophilic properties of biomolecules supplied as 3D-structuresAvailableFreeware
PRODOCK1999Cornell UniversityBased on Monte Carlo method plus energy minimizationNoAcademic
PSI-DOCK[9]2006Peking UniversityPose-Sensitive Inclined (PSI)-DOCKNoAcademic
PSO@AUTODOCK2007University of LeipzigParticle Swarm Optimization (PSO) algorithms varCPSO and varCPSO-ls are suited for rapid docking of highly flexible ligandsNoAcademic
PythDock2011Hanyang UniversityHeuristic docking program that uses Python programming language with a simple scoring function and a population based search engineNoAcademic
Q-Dock2008Georgia Institute of TechnologyLow-resolution flexible ligand docking with pocket-specific threading restraintsNoFreeware
QXP[10]1997Novartis Pharmaceuticals CorporationMonte Carlo perturbation with energy minimization in Cartesian spaceNoAcademic
rDock1998 (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 predictionNoOpen source (GNU LGPL) (formerly commercial, academic)
SANDOCK1998University of EdinburghGuided matching algorithmNoAcademic
Score2004Alessandro Pedretti & Giulio VistoliThe Score service allows to calculate some different docking scores of ligand-receptor complexAvailableFreeware
SEED1999University of ZurichAutomated docking of fragments with evaluation of free energy of binding including electrostatic solvation effects in the continuum dielectric approximation (generalized Born)NoOpen source (GNU GPL)
smina2012University of PittsburghA customized fork of AutoDock Vina with a better support scoring function and a high-performance energy minimizationNoOpen source (Apache License)
SODOCK2007Feng Chia University (Taiwan)Swarm optimization for highly flexible protein-ligand dockingNoAcademic
SOFTDocking1991University of California, BerkeleyMatching of molecular surface cubesNoAcademic
Surflex-Dock2003TriposBased on an idealized active site ligand (a protomol)NoCommercial
SwissDock2011Swiss Institute of BioinformaticsWebservice to predict interaction between a protein and a small molecule ligandAvailableFree to use webservice for academic usage
VoteDock2011University of WarsawConsensus docking method for prediction of protein-ligand interactionsNoAcademic
YUCCA2005Virginia TechRigid protein-small-molecule dockingNoAcademic

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.
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