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 scien ...

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

GNU General Public License The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end users the Four Freedoms (Free software), four freedoms to run, study, share, and modify the software. The license was th ...

. AutoDock is one of the most cited docking software applications in the research community. It is used by the

FightAIDS@Home FightAIDS@Home ("Fight AIDS at home") is a volunteer computing project operated by the Olson Laboratory at The Scripps Research Institute. It runs on internet-connected home computers, and since July 2013 also runs on Android smartphones and tabl ...

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 tackle scientific research that benefits humanity. Launched on November 16, 2004, with proprietary Grid MP client from United Devices and adding ...

, to search for antivirals against

HIV/AIDS Human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS) is a spectrum of conditions caused by infection with the human immunodeficiency virus (HIV), a retrovirus. Following initial infection an individual ...

and

COVID-19 Coronavirus disease 2019 (COVID-19) is a contagious disease caused by a virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The first known case was COVID-19 pandemic in Hubei, identified in Wuhan, China, in December ...

. 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. Both AutoDock and Vina are currently maintained by

Scripps Research Scripps Research, previously known as The Scripps Research Institute (TSRI), is a nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California, the institu ...

, 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 ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which ...

Mac OS X macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac (computer), Mac computers. Within the market of ...

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 and ...

, and

Microsoft Windows Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for serv ...

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

Debian Debian (), also known as Debian GNU/Linux, is a Linux distribution composed of free and open-source software, developed by the community-supported Debian Project, which was established by Ian Murdock on August 16, 1993. The first version of D ...

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, and

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. Compiling the application in native

64-bit In computer architecture, 64-bit Integer (computer science), integers, memory addresses, or other Data (computing), data units are those that are 64 bits wide. Also, 64-bit central processing unit, CPUs and arithmetic logic unit, ALUs are those ...

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 framework for writing programs that execute across heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), field-progra ...

and

CUDA CUDA (or Compute Unified Device Architecture) is a parallel computing platform and application programming interface (API) that allows software to use certain types of graphics processing units (GPUs) for general purpose processing, an approach ca ...

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 CorporationOfficially written as NVIDIA and stylized in its logo as VIDIA with the lowercase "n" the same height as the uppercase "VIDIA"; formerly stylized as VIDIA with a large italicized lowercase "n" on products from the mid 1990s to ...

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
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