AutoDock

Source: Wikipedia, the free encyclopedia.
AutoDock and AutoDock Vina
Developer(s)Scripps Research
Initial release1989; 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
SGI IRIX, and Microsoft Windows
PlatformMany
Available inEnglish
TypeProtein–ligand docking
LicenseGPL (AutoDock), Apache License (AutoDock Vina)
Websiteautodock.scripps.edu (AutoDock) vina.scripps.edu (AutoDock Vina)

AutoDock is a

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.

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]

  • 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.[6][7][9][10]

Platform support

AutoDock runs on

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.[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 Vina

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]

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.[21]
  • Off-Target Pipeline allows integration of AutoDock within bigger projects.[22]
  • Consensus Scoring ToolKit provides rescoring of AutoDock Vina poses with multiple scoring functions and calibration of consensus scoring equations.[23]
  • VSLAB is a VMD plug-in that allows the use of AutoDock directly from VMD.[24]
  • 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.[25]
  • POAP is a shell-script-based tool which automates AutoDock for virtual screening from ligand preparation to post docking analysis.[26]
  • 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.[27]

FPGA acceleration

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]

See also

References

  1. S2CID 21569704
    .
  2. ^ "We want to stop pandemics in their tracks". IBM. 2020-04-01. Retrieved 2020-04-04.
  3. ^
    PMID 19499576
    .
  4. ^ "The Center for Computational Structural Biology". The Center for Computational Structural Biology. 2020-05-15. Retrieved 2020-05-15.
  5. ^ "Arthur Olson | Scripps Research". www.scripps.edu. Retrieved 2019-05-22.
  6. ^
    PMID 32808340
    .
  7. ^ .
  8. .
  9. ^ a b Gupta G (2020-05-26). "Racing the Clock, COVID Killer Sought Among a Billion Molecules". Nvidia. Archived from the original on 2020-06-11. Retrieved 2020-09-26.
  10. ^ "Molecules in Motion: Computer Simulations Lead to a Better Understanding of Protein Structures". www.nsf.gov. Retrieved 2019-05-22.
  11. ^ "AutoDock — AutoDock". autodock.scripps.edu. Retrieved 2019-05-22.
  12. ^ "Debian Package Tracker - autodocksuite". tracker.debian.org. Retrieved 2019-05-22.
  13. ^ "Debian Package Tracker - autodock-vina". tracker.debian.org. Retrieved 2019-05-22.
  14. ^ "Package autodocksuite". apps.fedoraproject.org. Archived from the original on 2020-01-01. Retrieved 2019-05-22.
  15. ^ "AUR (en) - autodock-vina". aur.archlinux.org. Retrieved 2019-05-22.
  16. ^ "How to compile autodock as native 64 bit windows application — AutoDock". autodock.scripps.edu. Retrieved 2019-05-22.
  17. ^ a b GitHub - ccsb-scripps/AutoDock-GPU: AutoDock for GPUs using OpenCL., Center for Computational Structural Biology, 2019-08-23, retrieved 2019-09-15
  18. ^ "Windows 10 or Linux". World Community Grid. 2019-10-31. Retrieved 2020-04-04.
  19. ^ ccsb-scripps/AutoDock-Vina, Center for Computational Structural Biology, 2021-07-20, retrieved 2021-07-20
  20. PMID 34278794
    .
  21. ^ "smina". SourceForge. Retrieved 2019-09-15.
  22. ^ "Off-Target Pipeline". sites.google.com. Retrieved 2019-05-22.
  23. ^ "Consensus Scoring ToolKit | consensus scoring optimization for protein ligand docking". Retrieved 2019-05-22.
  24. ^ "Turning Docking and Virtual Screening as simple as it can get..." www.fc.up.pt. Retrieved 2019-05-22.
  25. ^ "Welcome to the PyRx Website".
  26. S2CID 3849603
    .
  27. .
  28. ^ "Omixon - Products - Docking". 2010-03-05. Archived from the original on 2010-03-05. Retrieved 2019-05-22.
  29. . Retrieved 2019-05-22.

External links