AutoDock is a molecular modeling

Molecular modelling

Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...

 simulation software. Since 2009, it has been open source

Open source

The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...

 and is free for non-commercial usage. It is especially effective for Protein-ligand docking

Protein-ligand docking

Protein–ligand docking is a molecular modelling technique. The goal of protein-ligand docking is to predict the position and orientation of a ligand when it is bound to a protein receptor or enzyme...

.

About

AutoDock is one of the most cited docking softwares in the research community. It is a base for the FightAIDS@Home

FightAIDS@Home

FightAIDS@Home is a distributed computing project for internet-connected home computers, operated by the Olson Laboratory at The Scripps Research Institute...

 project run by World Community Grid

World Community Grid

World Community Grid is an effort to create the world's largest public computing grid to tackle scientific research projects that benefit humanity...

. In February 2007, a search of the ISI Citation Index showed more than 1100 publications have been cited using the primary AutoDock method papers. As of 2009, this number surpassed 1200.

AutoDock is currently maintained by The Scripps Research Institute

The Scripps Research Institute

The Scripps Research Institute is an American medical research facility that focuses on research in the basic biomedical sciences. Headquartered in La Jolla, California, with a sister facility in Jupiter, Florida, the institute is home to 3,000 scientists, technicians, graduate students, and...

 and Olson Laboratory.

Programs

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.

AutoDock has an improved version, AutoDock Vina which has an improved local search routine and allows the use of multicore/multi-CPU computer setups.

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

Third party improvements

As an open source project, AutoDock has gained several third party improved versions such as:

• GPU improved calculation routines
• SSE improved calculation routines
• Integration within bigger projects: OFF-TARGET PIPELINE http://personalpages.manchester.ac.uk/postgrad/Thomas.Evangelidis/ug/Intro.html

64 bit native compilation

Compiling application in native 64 bit mode enables faster floating point operation of the software. Please refer to: http://autodock.scripps.edu/faqs-help/how-to/how-to-compile-autodock-as-native-64-bit-windows-application

FPGA acceleration

Using general programmable chips as coprocessor, speedups were within range 10x-100x the speed of standard Intel Dual Core 2Ghz CPU.

• OMIXON experimental product. Please refer to: http://www.omixon.com/omixon/faces/prod_docking.jsp
• Budapest University of Technology and Economics
  Budapest University of Technology and Economics
  The Budapest University of Technology and Economics , in hungarian abbreviated as BME, English official abbreviation BUTE, is the most significant University of Technology in Hungary and is also one of the oldest Institutes of Technology in the world, having been founded in 1782.-History:BME is...
  
  Please refer to: http://mycite.omikk.bme.hu/doc/104429.pdf

Others

VSLAB is a VMD plug-in that allows the use of autodock directly from VMD. This program is very easy to use and allows almost anyone to dock a ligand into a protein. More details can be found at http://www.fc.up.pt/pessoas/nscerque/vsLab/vLab/HomePage.html.