AutoDock is a molecular modeling simulation software. It is especially effective for protein-ligand docking. AutoDock 4 is available under the GNU General Public License. AutoDock is one of the most cited docking software applications in the research community.[1] It is used by the FightAIDS@Home and OpenPandemics - COVID-19 projects run at World Community Grid, to search for antivirals against HIV/AIDS and COVID-19.[2] 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.
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| Developer(s) | Scripps Research |
|---|---|
| Initial release | 1989; 35 years ago (1989) |
| Stable release | 4.2.6 (AutoDock), 1.2.0 (AutoDock Vina) / 2014; 10 years ago (2014) (AutoDock), 2021; 3 years ago (2021) (AutoDock Vina) |
| Written in | C++, C |
| Operating system | Linux, Mac OS X, SGI IRIX, and Microsoft Windows |
| Platform | Many |
| Available in | English |
| Type | Protein–ligand docking |
| License | GPL (AutoDock), Apache License (AutoDock Vina) |
| Website | autodock |
AutoDock Vina is a successor of AutoDock, significantly improved in terms of accuracy and performance.[3] It is available under the Apache license.
Both AutoDock and Vina are currently maintained by Scripps Research, specifically the Center for Computational Structural Biology (CCSB) led by Dr. Arthur J. Olson[4][5]
AutoDock is widely used and played a role in the development of the first clinically approved HIV-1 integrase inhibitor by Merck & Co.[6][7]
AutoDock consists of two main programs:[8]
Usage of AutoDock has contributed to the discovery of several drugs, including HIV1 integrase inhibitors.[6][7][9][10]
AutoDock runs on Linux, Mac OS X, SGI IRIX, and Microsoft Windows.[11] It is available as a package in several Linux distributions, including Debian,[12][13] Fedora,[14] and Arch Linux.[15]
Compiling the application in native 64-bit mode on Microsoft Windows enables faster floating-point operation of the software.[16]
Improved calculation routines using OpenCL and CUDA have been developed by the AutoDock Scripps research team.[17]
It results in observed speedups of up to 4x (quad-core CPU) and 56x (GPU) over the original serial AutoDock 4.2 (Solis-Wets) on CPU.
The CUDA version was developed in a collaboration between the Scripps research team and Nvidia[9][17] while the OpenCL version was further optimized with support from the IBM World Community Grid team.
AutoDock has a successor, AutoDock Vina, which has an improved local search routine and makes use of multicore/multi-CPU computer setups.[3]
AutoDock Vina has been noted for running significantly faster under 64-bit Linux operating systems in several World Community Grid projects that used the software.[18]
AutoDock Vina is currently on version 1.2, released in July 2021.[19][20]
As an open source project, AutoDock has gained several third-party improved versions such as:
Using general programmable chips as co-processors, specifically the OMIXON experimental product,[28] speedup was within the range 10x-100x the speed of standard Intel Dual Core 2 GHz CPU.[29]