AutoDock

BioCodeKb - Bioinformatics Knowledgebase

AutoDock is molecular modeling simulation software. It is especially effective for protein-ligand docking. AutoDock 4 is available under the GNU General Public License.


AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.


AutoDock is one of the most cited docking software applications in the research community. In February 2007, a search of the ISI Citation Index showed more than 1,100 publications had been cited using the primary AutoDock method papers. As of 2009, this number surpassed 1,200.


AutoDock Vina is a successor of AutoDock, significantly improved in terms of accuracy and performance. It is available under the Apache license. In addition to using them for docking, the atomic affinity grids can be visualized. This can help, for example, to guide organic synthetic chemists design better binders.


Both AutoDock and Vina are currently maintained by Scripps Research, specifically the Center for Computational Structural Biology (CCSB) led by Dr. Arthur J. Olson.


AutoDock consists of two main programs:

  • AutoDock for docking of the ligand to a set of grids describing the target protein.

  • AutoGrid for pre-calculating these grids. Furthermore, it generates an electrostatic potential grid map and a desolvation map. The full set of grid maps and the flexible part of the receptor are used by AutoDock to guide the docking process of the selected ligands.


Usage of AutoDock has contributed to the discovery of many drugs, including HIV1 integrase inhibitors.


AutoDock runs on Linux, Mac OS X, SGI IRIX, and Microsoft Windows. It is available as a package in several Linux distributions, including Debian, Fedora, and Arch Linux.


AutoDock offers a variety of search algorithms to explore a given docking problem. These include Monte Carlo Simulated Annealing (SA); a Genetic Algorithm (GA); and a hybrid local search GA, also known as the Lamarckian Genetic Algorithm (LGA). In general, the LGA performs the best out of SA, GA, and LGA, in finding the lowest energy of the system.


Compiling the application in native 64-bit mode on Microsoft Windows enables faster floating-point operation of the software.


AutoDock is the first docking package to model the ligand with full conformational flexibility.


AutoDock's main strengths are

  1. receptor flexibility

  2. blind-docking

  3. precalculated grid maps on a binding site

  4. free-energy scoring function based on linear regression analysis, the AMBER force field, and a large set of protein–ligand complexes with known inhibition constants

  5. good correlation between predicted inhibition constants and experimental data. [


AutoDock Vina does not require choosing atom types and pre-calculating grid maps for them. Instead, it calculates the grids internally, for the atom types that are needed, and it does this virtually instantly.


We have also developed a graphical user interface called AutoDockTools, or ADT for short, which amongst other things helps to set up which bonds will treated as rotatable in the ligand and to analyze dockings.


AutoDock has applications in:

  • X-ray crystallography

  • structure-based drug design

  • lead optimization

  • virtual screening (HTS)

  • combinatorial library design

  • protein-protein docking

  • chemical mechanism studies

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