Molecular docking

PLANTS - Protein-Ligand ANT System
http://www.tcd.uni-konstanz.de/research/plants.php

A docking algorithm based on a class of stochastic optimization algorithms called ant colony optimization (ACO)

GOLD
http://www.ccdc.cam.ac.uk/products/life_sciences/gold

A genetic algorithm based protein-ligand docking program provided as part of the GOLD Suite

HYBRID - Ligand guided docking
http://www.eyesopen.com/docs/oedocking/current/html/hybrid.html#hybrid

A program that uses the information present in the structure of the protein and the bound ligand to enhance docking performance

FITTED - Flexibility Induced Through Targeted Evolutionary Description
http://fitted.ca/index.php?option=com_content&task=view&id=50&Itemid=40

A docking tool based on a pharmacophore-oriented docking method combined with a genetic algorithm based approach

DOCK
http://dock.compbio.ucsf.edu

An algorithm to address rigid body docking using a geometric matching algorithm

ClusPro - Protein-protein docking
http://cluspro.bu.edu http://nrc.bu.edu/cluster

A fully automated, web-based program for the computational docking of protein structures, using the coordinate files of two protein structures or the PDB codes

AutoDock
http://autodock.scripps.edu

A suite of automated docking tools consisting of two generations of software: AutoDock 4 and AutoDock Vina.

ADAM
http://www.immd.co.jp/en/product_2.html

A tool, that can predict the stable binding mode of flexible ligand molecule to target macromolecule

AutoDock Vina
http://vina.scripps.edu

A program for drug discovery, molecular docking and virtual screening

PatchDock - Molecular Docking Algorithm Based on Shape Complementarity Principles
http://bioinfo3d.cs.tau.ac.il/PatchDock

An algorithm for molecular docking based on shape complementarity principles, inspired by object recognition and image segmentation techniques

FRED - Fast exhaustive docking
http://www.eyesopen.com/docs/oedocking/current/html/fred.html

A program that uses an exhaustive search algorithm to dock molecules from a multiconformer database into a receptor site

HADDOCK - High Ambiguity Driven biomolecular DOCKing
http://www.nmr.chem.uu.nl/haddock

A protein-protein docking approach that makes use of biochemical and/or biophysical interaction data

POSIT - Ligand guided pose prediction
http://www.eyesopen.com/docs/posit/current/html/theory.html

A program designed to use bound ligand information to improve pose prediction

DockingServer
http://www.dockingserver.com

A web-based interface that can be used for docking and analysis of single ligands as well as for high throughput docking of ligand libraries to target proteins

GEMDOCK - Generic Evolutionary Method for molecular DOCKing
http://gemdock.life.nctu.edu.tw/dock

A evolutionary based method for computing a ligand conformation and orientation relative to the active site of the target protein

ICM-Docking
http://www.molsoft.com/docking.html

A pseudo-Brownian sampling and local minimization based docking method and provides tools for ligand-protein docking, peptide-protein docking, and protein-protein docking, including interactive graphics tools

iGEMDOCK
http://gemdock.life.nctu.edu.tw/dock/igemdock.php

A graphical environment for docking, virtual screening, and post-screening analysis

Magnet
http://www.metaphorics.com/products/magnet

A program for filtering docking results and to select those ligands which shows specified interactions with the target protein

URL not working as on 15 Nov 2016

SymmDock - Prediction of Complexes with Cn Symmetry by Geometry Based Docking
http://bioinfo3d.cs.tau.ac.il/SymmDock

A geometry based docking algorithm for predicting of a cyclically symmetric complex

3DLigandSite - Ligand binding site prediction Server
http://www.sbg.bio.ic.ac.uk/~3dligandsite

An automated method for predicting the ligand binding sites using a sequence or a protein structure as query

BetaDock
http://voronoi.hanyang.ac.kr/software.htm

A simulation software based on the theory of Beta-complex

eHiTS - Electronic High Throughput Screening
http://www.simbiosys.ca/ehits

A search based docking program

GlamDock
http://www.chil2.de/Glamdock.html

A structure based docking algorithm

Hex
http://hex.loria.fr

An interactive protein docking and molecular superposition program, that can take protein and DNA structures in PDB format, and small-molecule SDF files

iScreen
http://iscreen.cmu.edu.tw

A cloud-computing based web server for virtual screening and de novo drug designing based on TCM database

ParDOCK
http://www.scfbio-iitd.res.in/dock/pardock.jsp

An all-atom energy based Monte Carlo, rigid protein ligand docking, which predicts the binding mode of the ligand in receptor target site

SwissDock
http://swissdock.vital-it.ch

A web server for the docking of protein and small molecule, and is based on the docking software EADock DSS

TarFisDock - Target Fishing Dock
http://www.dddc.ac.cn/tarfisdock

A web server for identifying drug targets by docking a small molecule to the protein targets present in the Potential Drug Target Database

ADDock
http://www.biodelight.com.tw/English/addock_index.html

An anchor dependent molecular docking tool for docking of small flexible molecules to rigid protein receptors

100

ATOME
http://atome.cbs.cnrs.fr/AT2/meta.html

A pipeline for protein structure modeling and small ligand docking based on comparative analyses.

100

AuPosSOM
https://www.biomedicale.univ-paris5.fr/aupossom

A virtual screening program for the automatic analysis of docked structures

100

BSP-SLIM
http://zhanglab.ccmb.med.umich.edu/BSP-SLIM

A web-server for low-resolution docking on predicted protein structures

100

DOCK Blaster
http://blaster.docking.org

A server for structure-based ligand discovery, that uses DOCK as the docking program and various ZINC database subsets as the database

100

DockIt
http://www.metaphorics.com/products/dockit.html

A tool for docking of small molecules with macromolecular targets for various applications including combinatorial chemistry, virtual library screening and design, and target identification

100

DockVision
http://dockvision.com

A docking package that integrates, Monte Carlo, Genetic Algorithm, and database screening docking algorithms and various other tools

100

The given URL opens a non-English website, as on 14 Nov 2016

A method for flexible refinement and re-scoring of rigid-body protein-protein docking solutions

100

Fleksy - A flexible approach to induced fit docking
http://www.cmbi.ru.nl/software/fleksy

A approach that considers both ligand and receptor flexibility in small molecule docking

100

FlexX
http://www.biosolveit.de/flexx

A structure based docking tool

100

FLIPDock
http://flipdock.scripps.edu/what-is-flipdock

A molecular docking program for flexible ligand and flexible receptor

100

GPCRautomodel
http://genome.jouy.inra.fr/GPCRautomdl/cgi-bin/welcome.pl

A web-service for automatic modeling of G-protein coupled receptors based on fold recognition techniques

100

GRAMM-X
http://vakser.bioinformatics.ku.edu/resources/gramm/grammx

A web server for protein-protein docking

100

HomDock
http://www.chil2.de/HomDock.html

A similarity based docking tool with combination of the ligand based GMA molecular alignment tool and GlamDock docking tool

100

idTarget
http://idtarget.rcas.sinica.edu.tw

A web server for identifying small chemical bio-molecular targets with robust scoring functions and a divide-and-conquer docking approach

100

kinDOCK: A Ligand Transposition Server
http://abcis.cbs.cnrs.fr/LIGBASE_SERV_WEB/PHP/kindock.php

A web-server for comparative docking of ligands into the ATP-binding site of a protein kinase target.

100

Lead Finder
http://www.moltech.ru

A program for molecular docking, virtual screening and evaluation of ligand binding and biological activity

100

MEDock - Maximum-Entropy based Docking
http://medock.csie.ntu.edu.tw

A maximum-entropy based docking server for prediction of ligand binding sites

100

URL not working as on 9 Feb 2015 (confirmed on 15 Nov 2016)

MVD - Molegro Virtual Docker
http://www.molegro.com/mvd-product.php

#An integrated platform for all aspects of the docking process, from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands

100

ParaDocks - Parallel Docking Suite
http://www.paradocks.org

A framework for molecular docking tool focused on docking small, drug-like molecules to a rigid receptor, employing either the knowledge-based potential PMF04 or the empirical energy function p-Score

100

Quantum.Ligand.Dock
http://87.116.85.141/LigandDock.html

A method for in silico prediction of protein-ligand interactions via high-performance docking code

100

URL not working as on 9 Feb 2015 (confirmed on 15 Nov 2016)

Rosetta FlexPepDock - High resolution modeling of peptide-protein interactions
http://flexpepdock.furmanlab.cs.huji.ac.il/index.php

A tool for high-resolution modeling of peptide-protein docking

100

RosettaLigand
http://www.rosettacommons.org/software

A program for small molecule-protein docking

100

Surflex-Dock
http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=Surflex_Dock