AutoDock explained

AutoDock and AutoDock Vina
Developer:Scripps Research
Latest Release Version:4.2.6 (AutoDock), 1.2.0 (AutoDock Vina)
Latest Release Date: (AutoDock), (AutoDock Vina)
Programming Language:C++, C
Operating System:Linux, Mac OS X, SGI IRIX, and Microsoft Windows
Platform:Many
Language:English
Genre:Protein–ligand docking
License:GPL (AutoDock), Apache License (AutoDock Vina)
Website: (AutoDock) (AutoDock Vina)

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.

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]

Programs

AutoDock consists of two main programs:[8]

Usage of AutoDock has contributed to the discovery of several drugs, including HIV1 integrase inhibitors.[9] [10]

Platform support

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 versions

AutoDock for GPUs

Improved calculation routines using OpenCL and CUDA 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 while the OpenCL version was further optimized with support from the IBM World Community Grid 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.[17]

AutoDock Vina is currently on version 1.2, released in July 2021.[18]

Third-party improvements and tools

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

FPGA acceleration

Using general programmable chips as co-processors, specifically the OMIXON experimental product,[26] speedup was within the range 10x-100x the speed of standard Intel Dual Core 2 GHz CPU.[27]

See also

External links

Notes and References

  1. Sousa SF, Fernandes PA, Ramos MJ . Protein-ligand docking: current status and future challenges . Proteins . 65 . 1 . 15–26 . October 2006 . 16862531 . 10.1002/prot.21082 . 21569704 .
  2. Web site: We want to stop pandemics in their tracks. . 2020-04-01. IBM. 2020-04-04.
  3. Trott O, Olson AJ . AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading . Journal of Computational Chemistry . 31 . 2 . 455–61 . January 2010 . 19499576 . 3041641 . 10.1002/jcc.21334 .
  4. Web site: The Center for Computational Structural Biology. 2020-05-15. The Center for Computational Structural Biology. 2020-05-15.
  5. Web site: Arthur Olson Scripps Research. www.scripps.edu. 2019-05-22.
  6. Goodsell DS, Sanner MF, Olson AJ, Forli S . The AutoDock suite at 30 . Protein Science . August 2020 . 30 . 1 . 31–43 . 32808340 . 10.1002/pro.3934 . 7737764 .
  7. Schames JR, Henchman RH, Siegel JS, Sotriffer CA, Ni H, McCammon JA . Discovery of a novel binding trench in HIV integrase . Journal of Medicinal Chemistry . 47 . 8 . 1879–81 . April 2004 . 15055986 . 10.1021/jm0341913 .
  8. Park H, Lee J, Lee S . Critical assessment of the automated AutoDock as a new docking tool for virtual screening . Proteins . 65 . 3 . 549–54 . November 2006 . 16988956 . 10.1002/prot.21183 . 28351121 .
  9. Web site: Gupta G . 2020-05-26. Racing the Clock, COVID Killer Sought Among a Billion Molecules. live. https://web.archive.org/web/20200611183756/https://blogs.nvidia.com/blog/2020/05/26/covid-autodock-summit-ornl/ . 2020-06-11 . 2020-09-26. Nvidia.
  10. Web site: Molecules in Motion: Computer Simulations Lead to a Better Understanding of Protein Structures. www.nsf.gov. 29 July 2005 . English. 2019-05-22.
  11. Web site: AutoDock — AutoDock. autodock.scripps.edu. 2019-05-22.
  12. Web site: Debian Package Tracker - autodocksuite. tracker.debian.org. 2019-05-22.
  13. Web site: Debian Package Tracker - autodock-vina. tracker.debian.org. 2019-05-22.
  14. Web site: Package autodocksuite. apps.fedoraproject.org. 2019-05-22. 2020-01-01. https://web.archive.org/web/20200101212814/https://apps.fedoraproject.org/packages/autodocksuite. dead.
  15. Web site: AUR (en) - autodock-vina. aur.archlinux.org. 2019-05-22.
  16. Web site: How to compile autodock as native 64 bit windows application — AutoDock. autodock.scripps.edu. 2019-05-22.
  17. Web site: Windows 10 or Linux . 2019-10-31. World Community Grid. 2020-04-04.
  18. Eberhardt. Jerome. Santos-Martins. Diogo. Tillack. Andreas F.. Forli. Stefano. 2021-07-19. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. Journal of Chemical Information and Modeling. 61. 8. 3891–3898. 10.1021/acs.jcim.1c00203. 34278794. 1549-9596. 10683950.
  19. Web site: smina. SourceForge. en. 2019-09-15.
  20. Web site: Off-Target Pipeline. sites.google.com. 2019-05-22.
  21. Web site: Consensus Scoring ToolKit consensus scoring optimization for protein ligand docking. en-US. 2019-05-22.
  22. Web site: Turning Docking and Virtual Screening as simple as it can get.... www.fc.up.pt. 2019-05-22.
  23. Web site: Welcome to the PyRx Website.
  24. Samdani A, Vetrivel U . POAP: A GNU parallel based multithreaded pipeline of open babel and AutoDock suite for boosted high throughput virtual screening . Computational Biology and Chemistry . 74 . 39–48 . June 2018 . 29533817 . 10.1016/j.compbiolchem.2018.02.012 . 3849603 .
  25. Gorgulla C, Boeszoermenyi A, Wang ZF, Fischer PD, Coote PW, Padmanabha Das KM, Malets YS, Radchenko DS, Moroz YS, Scott DA, Fackeldey K, Hoffmann M, Iavniuk I, Wagner G, Arthanari H . 6 . An open-source drug discovery platform enables ultra-large virtual screens . Nature . 580 . 7805 . 663–668 . April 2020 . 32152607 . 10.1038/s41586-020-2117-z . 212653203 . 2020Natur.580..663G . 8352709 .
  26. Web site: Omixon - Products - Docking. https://web.archive.org/web/20100305073154/http://www.omixon.com/omixon/faces/prod_docking.jsp. dead. 2010-03-05. 2010-03-05. 2019-05-22.
  27. Book: FPGA-Based Acceleration of the AutoDock Molecular Docking Software. Pechan I . BME MDA, a Műegyetem Digitális Archivuma. 9783981375411. 2019-05-22.

This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "AutoDock".

Except where otherwise indicated, Everything.Explained.Today is © Copyright 2009-2024, A B Cryer, All Rights Reserved. Cookie policy.