List of protein-ligand docking software

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The number of notable 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 notable 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
2011 Mcule Docking predicts the binding orientation and affinity of a ligand to a target Yes Free to use webservice
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
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)
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
HEX 2008 Dave Ritchie[7] An interactive protein docking and molecular superposition program Yes Free for Academic and Government and HEX Server [8] Available
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[9] 2018 Barcelona Supercomputing Center Protein-protein, protein-DNA, protein-peptide docking using different scoring functions, backbone flexibility modeled by ANM and written in Python3 and Rust_(programming_language) Yes 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 2.0[10] 2019 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[11] 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[12] 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[13] 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[14] 1997 Novartis Pharmaceuticals Corporation Monte Carlo perturbation with energy minimization in Cartesian space No Academic
rDock 1998 (commercial)
2006 (academic)[15]
2012 (open source)[16]		 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 (in American English). Retrieved 2019-05-22.
  5. ^ "GalaxyWEB". galaxy.seoklab.org. Retrieved 2019-05-22.
  6. ^ "HADDOCK2.2 licensing". Bonvin Lab. Retrieved 2019-05-24.
  7. ^ "HEX". members.loria.fr.
  8. ^ "HEX Server". hexserver.loria.fr.
  9. ^ Jimenez-Garcia, Brian (2019-09-28), Protein docking framework based on the GSO algorithm: lightdock/lightdock, retrieved 2019-09-28
  10. ^ Wang, Jian; Dokholyan, Nikolay V. (24 June 2019). "MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints". Journal of Chemical Information and Modeling. 59 (6): 2509–2515. doi:10.1021/acs.jcim.8b00905. PMC 6597311. PMID 30946779.
  11. ^ Baldauf, Carsten (2017-08-22), Framework for molecular docking with population-based metaheuristics: cbaldauf/paradocks, retrieved 2019-06-01
  12. ^ "PARDock | SCFBio".
  13. ^ Pei, Jianfeng; Wang, Qi; Liu, Zhenming; Li, Qingliang; Yang, Kun; Lai, Luhua (4 January 2006). "PSI-DOCK: Towards highly efficient and accurate flexible ligand docking". Proteins: Structure, Function, and Bioinformatics. 62 (4): 934–946. doi:10.1002/prot.20790. PMID 16395666. S2CID 5715684.
  14. ^ Mcmartin, Colin; Bohacek, Regine S. (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. PMID 9334900. S2CID 31660790.
  15. ^ "rDock". www.ysbl.york.ac.uk. Retrieved 2020-02-12.
  16. ^ "About | rDock" (in American English). Retrieved 2020-02-12.

External links[]

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