AutoDock

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AutoDock and AutoDock Vina
Developer(s)Scripps Research
Initial release1989; 31 years ago (1989)
Stable release
4.2.6 (AutoDock), 1.1.2 (AutoDock Vina) / 2014; 6 years ago (2014) (AutoDock), 2011; 9 years ago (2011) (AutoDock Vina)
Written inC++, C
Operating systemLinux, Mac OS X, SGI IRIX, and Microsoft Windows
PlatformMany
Available inEnglish
TypeProtein–ligand docking
LicenseGPL (AutoDock), Apache License (AutoDock Vina)
Websiteccsb.scripps.edu/autodock (AutoDock) vina.scripps.edu (AutoDock Vina)

AutoDock is 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 a base for 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][8]

Programs[edit]

AutoDock consists of two main programs:[9]

  • 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][8][10][11][12]

Platform support[edit]

AutoDock runs on Linux, Mac OS X, SGI IRIX, and Microsoft Windows.[13] It is available as a package in several Linux distributions, including Debian,[14][15] Fedora,[16] and Arch Linux.[17]

Compiling the application in native 64-bit mode on Microsoft Windows enables faster floating-point operation of the software.[18]

Improved versions[edit]

AutoDock for GPUs[edit]

Improved calculation routines using OpenCL and CUDA have been developed by the AutoDock Scripps research team.[19]

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. It is currently faster than the OpenCL version.[10][19]

AutoDock Vina[edit]

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[20]

Third-party improvements and tools[edit]

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[edit]

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[edit]

References[edit]

  1. ^ Sousa, Sérgio Filipe; Fernandes, Pedro Alexandrino; Ramos, Maria João (2006-07-21). "Protein-ligand docking: Current status and future challenges". Proteins: Structure, Function, and Bioinformatics. 65 (1): 15–26. doi:10.1002/prot.21082. ISSN 0887-3585. PMID 16862531.
  2. ^ "We want to stop pandemics in their tracks". IBM. 2020-04-01. Retrieved 2020-04-04.
  3. ^ a b Trott, O.; Olson, A.J. (2010), "AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading", Journal of Computational Chemistry, 31 (2): 455–461, doi:10.1002/jcc.21334, PMC 3041641, 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. ^ a b Goodsell, David S. (2020-08-17). "The AutoDock Suite at 30". Retrieved 2020-09-26.
  7. ^ a b Goodsell, David S. (2020-09-14). "The AutoDock suite at 30" (PDF). Forli Lab. Retrieved 2020-09-26.
  8. ^ a b Schames, Julie R. (2004-03-09). "Discovery of a Novel Binding Trench in HIV Integrase". Journal of Medicinal Chemistry. Retrieved 2020-09-26.
  9. ^ Hwangseo Park; Jinuk Lee; Sangyoub Lee (2006), "Critical assessment of the automated AutoDock as a new docking tool for virtual screening", Proteins: Structure, Function, and Bioinformatics, 65 (3): 549–554, doi:10.1002/prot.21183, PMID 16988956
  10. ^ a b Gupta, Geetika (2020-05-26). "Racing the Clock, COVID Killer Sought Among a Billion Molecules". Nvidia. Retrieved 2020-09-26.
  11. ^ Schames, Julie R.; Henchman, Richard H.; Siegel, Jay S.; Sotriffer, Christoph A.; Ni, Haihong; McCammon, J. Andrew (2004-03-04). "Discovery of a Novel Binding Trench in HIV Integrase". Journal of Medicinal Chemistry. 47 (8): 1879–1881. doi:10.1021/jm0341913. ISSN 0022-2623. PMID 15055986.
  12. ^ "Molecules in Motion: Computer Simulations Lead to a Better Understanding of Protein Structures". www.nsf.gov. Retrieved 2019-05-22.
  13. ^ "AutoDock — AutoDock". autodock.scripps.edu. Retrieved 2019-05-22.
  14. ^ "Debian Package Tracker - autodocksuite". tracker.debian.org. Retrieved 2019-05-22.
  15. ^ "Debian Package Tracker - autodock-vina". tracker.debian.org. Retrieved 2019-05-22.
  16. ^ "Package autodocksuite". apps.fedoraproject.org. Retrieved 2019-05-22.
  17. ^ "AUR (en) - autodock-vina". aur.archlinux.org. Retrieved 2019-05-22.
  18. ^ "How to compile autodock as native 64 bit windows application — AutoDock". autodock.scripps.edu. Retrieved 2019-05-22.
  19. ^ a b GitHub - ccsb-scripps/AutoDock-GPU: AutoDock for GPUs using OpenCL., Center for Computational Structural Biology, 2019-08-23, retrieved 2019-09-15
  20. ^ "Windows 10 or Linux". World Community Grid. 2019-10-31. Retrieved 2020-04-04.
  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. ^ Samdani, A.; Vetrivel, Umashankar (2018-06-01). "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. doi:10.1016/j.compbiolchem.2018.02.012. PMID 29533817.
  27. ^ Christoph Gorgulla; et al. (2020), "An open-source drug discovery platform enables ultra-large virtual screens", Nature, 580 (7805): 663–668, doi:10.1038/s41586-020-2117-z, PMID 32152607
  28. ^ "Omixon - Products - Docking". 2010-03-05. Archived from the original on 2010-03-05. Retrieved 2019-05-22.
  29. ^ Pechan, Imre. "FPGA-Based Acceleration of the AutoDock Molecular Docking Software". BME MDA, a Műegyetem Digitális Archivuma. Retrieved 2019-05-22.

External links[edit]