AutoDock is a

molecular modeling Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials scienc ...

simulation software. It is especially effective for protein-ligand docking. AutoDock 4 is available under the

GNU General Public License The GNU General Public Licenses (GNU GPL or simply GPL) are a series of widely used free software licenses, or ''copyleft'' licenses, that guarantee end users the freedom to run, study, share, or modify the software. The GPL was the first ...

. AutoDock is one of the most cited docking software applications in the research community. It is used by the FightAIDS@Home and OpenPandemics - COVID-19 projects run at

World Community Grid World Community Grid (WCG) is an effort to create the world's largest volunteer computing platform to perform scientific research that benefits humanity. Launched on November 16, 2004, with proprietary Grid MP client from United Devices and add ...

, to search for antivirals against

HIV/AIDS The HIV, human immunodeficiency virus (HIV) is a retrovirus that attacks the immune system. Without treatment, it can lead to a spectrum of conditions including acquired immunodeficiency syndrome (AIDS). It is a Preventive healthcare, pr ...

and

COVID-19 Coronavirus disease 2019 (COVID-19) is a contagious disease caused by the coronavirus SARS-CoV-2. In January 2020, the disease spread worldwide, resulting in the COVID-19 pandemic. The symptoms of COVID‑19 can vary but often include fever ...

. 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 The Apache License is a permissive free software license written by the Apache Software Foundation (ASF). It allows users to use the software for any purpose, to distribute it, to modify it, and to distribute modified versions of the software ...

. Both AutoDock and Vina are currently maintained by

Scripps Research Scripps Research is a nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California, the institute has over 170 laboratories employing 2,100 scientists, tec ...

, specifically the Center for Computational Structural Biology (CCSB) led by Dr. Arthur J. Olson AutoDock is widely used and played a role in the development of the first clinically approved HIV-1 integrase inhibitor by Merck & Co.

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

Platform support

AutoDock runs on

Linux Linux ( ) is a family of open source Unix-like operating systems based on the Linux kernel, an kernel (operating system), operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically package manager, pac ...

Mac OS X macOS, previously OS X and originally Mac OS X, is a Unix, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. With ...

SGI IRIX IRIX (, ) is a discontinued operating system developed by Silicon Graphics (SGI) to run on the company's proprietary MIPS workstations and servers. It is based on UNIX System V with BSD extensions. In IRIX, SGI originated the XFS file system an ...

, and

Microsoft Windows Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sec ...

. It is available as a package in several Linux distributions, including

Debian Debian () is a free and open-source software, free and open source Linux distribution, developed by the Debian Project, which was established by Ian Murdock in August 1993. Debian is one of the oldest operating systems based on the Linux kerne ...

Fedora A fedora () is a hat with a soft brim and indented crown.Kilgour, Ruth Edwards (1958). ''A Pageant of Hats Ancient and Modern''. R. M. McBride Company. It is typically creased lengthwise down the crown and "pinched" near the front on both sides ...

, and

Arch Linux Arch Linux () is an Open-source software, open source, rolling release Linux distribution. Arch Linux is kept up-to-date by regularly updating the individual pieces of software that it comprises. Arch Linux is intentionally minimal, and is meant ...

. Compiling the application in native

64-bit In computer architecture, 64-bit integers, memory addresses, or other data units are those that are 64 bits wide. Also, 64-bit central processing units (CPU) and arithmetic logic units (ALU) are those that are based on processor registers, a ...

mode on Microsoft Windows enables faster floating-point operation of the software.

Improved versions

AutoDock for GPUs

Improved calculation routines using

OpenCL OpenCL (Open Computing Language) is a software framework, framework for writing programs that execute across heterogeneous computing, heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), di ...

and

CUDA In computing, CUDA (Compute Unified Device Architecture) is a proprietary parallel computing platform and application programming interface (API) that allows software to use certain types of graphics processing units (GPUs) for accelerated gene ...

have been developed by the AutoDock Scripps research team. 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 Nvidia Corporation ( ) is an American multinational corporation and technology company headquartered in Santa Clara, California, and incorporated in Delaware. Founded in 1993 by Jensen Huang (president and CEO), Chris Malachowsky, and Curti ...

while the OpenCL version was further optimized with support from the IBM

team.

AutoDock Vina

AutoDock has a successor, AutoDock Vina, which has an improved local search routine and makes use of multicore/multi-CPU computer setups. 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. AutoDock Vina is currently on version 1.2, released in July 2021.

Third-party improvements and tools

As an open source project, AutoDock has gained several third-party improved versions such as: * Scoring and Minimization with AutoDock Vina (smina) is a fork of AutoDock Vina with improved support for scoring function development and energy minimization. * Off-Target Pipeline allows integration of AutoDock within bigger projects. * Consensus Scoring ToolKit provides rescoring of AutoDock Vina poses with multiple scoring functions and calibration of consensus scoring equations. * VSLAB is a VMD plug-in that allows the use of AutoDock directly from VMD. * PyRx provides a nice GUI for running virtual screening with AutoDock. PyRx includes a docking wizard and you can use it to run AutoDock Vina in the Cloud or HPC cluster. * POAP is a shell-script-based tool which automates AutoDock for virtual screening from ligand preparation to post docking analysis. * VirtualFlow allows to carry out ultra-large virtual screenings on computer clusters and the cloud using AutoDock Vina-based docking programs, allowing to routinely screen billions of compounds.

FPGA acceleration

Using general programmable chips as co-processors, specifically the OMIXON experimental product, speedup was within the range 10x-100x the speed of standard Intel Dual Core 2 GHz CPU.

References

External links

AutoDock homepageAutoDock Vina homepage
{{Chemistry software Molecular modelling software Molecular modelling Free and open-source software Free software programmed in C++ Free software programmed in C Software using the Apache license Software using the GNU General Public License