AutoDock

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 and AutoDock Vina
Developer(s)Scripps Research
Initial release1989 (1989)
Stable release
4.2.6 (AutoDock), 1.2.0 (AutoDock Vina) / 2014 (2014) (AutoDock), 2021 (2021) (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)
Websiteautodock.scripps.edu (AutoDock) vina.scripps.edu (AutoDock Vina)

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]

  • 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 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.[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. Sousa SF, Fernandes PA, Ramos MJ (October 2006). "Protein-ligand docking: current status and future challenges". Proteins. 65 (1): 15–26. doi:10.1002/prot.21082. PMID 16862531. S2CID 21569704.
  2. "We want to stop pandemics in their tracks". IBM. 2020-04-01. Retrieved 2020-04-04.
  3. Trott O, Olson AJ (January 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): 455–61. 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. Goodsell DS, Sanner MF, Olson AJ, Forli S (August 2020). "The AutoDock suite at 30". Protein Science. 30 (1): 31–43. doi:10.1002/pro.3934. PMC 7737764. PMID 32808340.
  7. Schames JR, Henchman RH, Siegel JS, Sotriffer CA, Ni H, McCammon JA (April 2004). "Discovery of a novel binding trench in HIV integrase". Journal of Medicinal Chemistry. 47 (8): 1879–81. doi:10.1021/jm0341913. PMID 15055986.
  8. Park H, Lee J, Lee S (November 2006). "Critical assessment of the automated AutoDock as a new docking tool for virtual screening". Proteins. 65 (3): 549–54. doi:10.1002/prot.21183. PMID 16988956. S2CID 28351121.
  9. 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. 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. 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. doi:10.1021/acs.jcim.1c00203. ISSN 1549-9596. 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. Samdani A, Vetrivel U (June 2018). "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. S2CID 3849603.
  27. Gorgulla C, Boeszoermenyi A, Wang ZF, Fischer PD, Coote PW, Padmanabha Das KM, et al. (April 2020). "An open-source drug discovery platform enables ultra-large virtual screens". Nature. 580 (7805): 663–668. Bibcode:2020Natur.580..663G. doi:10.1038/s41586-020-2117-z. PMC 8352709. PMID 32152607. S2CID 212653203.
  28. "Omixon - Products - Docking". 2010-03-05. Archived from the original on 2010-03-05. Retrieved 2019-05-22.
  29. Pechan I. FPGA-Based Acceleration of the AutoDock Molecular Docking Software. ISBN 9783981375411. Retrieved 2019-05-22. {{cite book}}: |website= ignored (help)
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