Open main menu

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.

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 Available Basic free version
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 Available 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
AutoDock Vina 2010 The Scripps Research Institute New generation of AutoDock No Open source
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 and as a web server. Available Freeware for academic use
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 Available 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 aligment, local combinatorial induced-fit No Academic
EADock 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 Available Free 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
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 Free 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 Free 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
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 Free 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 Freeware
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
LigandFit 2003 BioVia CHARMm based docking program No Commercial
LigDockCSA 2011 Seoul National University Protein-ligand docking using conformational space annealing No Academic
LightDock 2018 Barcelona Supercomputing Center Protein-protein, protein-DNA, protein-peptide docking using different scoring functions and backbone flexibility modeled by ANM No Open Source
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
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
MolDock 2006 Molegro ApS Based on a new heuristic search algorithm that combines differential evolution with a cavity prediction algorithm No Academic
MS-DOCK 2008 INSERM Multi-stage docking/scoring protocol No Academic
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 Free 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 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 1997 Novartis Pharmaceuticals Corporation Monte Carlo perturbation with energy minimization in Cartesian space No Academic
rDock 2013 University of York/ Open source project HTVS of small molecules against proteins and nucleic acids No Open source
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
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 webservice for academic use
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
MOLS 2.0 2016 University of Madras Rigid protein-small-molecule docking,Flexible protein-peptide docking No Open Source