AutoDock

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AutoDock and AutoDock Vina
Developer(s)The Scripps Research Institute
Initial release1989; 30 years ago (1989)
Stable release
4.2.6 (AutoDock), 1.1.2 (AutoDock Vina) / 2014; 5 years ago (2014) (AutoDock), 2011; 8 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)
Websiteautodock.scripps.edu (AutoDock) vina.scripps.edu (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 in the research community.[1] It is a base for the FightAIDS@Home project run by World Community Grid. In February 2007, a search of the ISI Citation Index showed more than 1,100 publications have 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.[2] It is available under the Apache license.

Both AutoDock and Vina are currently maintained by The Scripps Research Institute, specifically The Molecular Graphics Laboratory (Dr. Arthur J. Olson).[3][4]

Programs[edit]

AutoDock consists of two main programs:[5]

  • 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]

Platform support[edit]

AutoDock runs on Linux, Mac OS X, SGI IRIX, and Microsoft Windows.[8] It is available as a package in several Linux distributions, including Debian[9][10], Fedora[11], and Arch Linux[12].

Compiling the application in native 64-bit mode on Microsoft Windows enables faster floating-point operation of the software.[13]

Improved versions[edit]

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.[2]

Third-party improvements and tools[edit]

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

  • Improved calculation routines on the GPU using OpenCL.[14]
  • Scoring and Minimization with AutoDock Vina (smina) is a fork of AutoDock Vina with improved support for scoring function development and energy minimization.[15]
  • Off-Target Pipeline allows integration of AutoDock within bigger projects.[16]
  • Consensus Scoring ToolKit provides rescoring of AutoDock Vina poses with multiple scoring functions and calibration of consensus scoring equations.[17]
  • VSLAB is a VMD plug-in that allows the use of AutoDock directly from VMD.[18]
  • 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.[19]
  • POAP is an shell script based tool which automates AutoDock for virtual screening right from ligand preparation to post docking analysis.[20]

FPGA acceleration[edit]

Using general programmable chips as co-processors, specifically OMIXON experimental product[21], speedup was within the range 10x-100x the speed of standard Intel Dual Core 2 GHz CPU.[22]

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. ^ 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
  3. ^ "The Molecular Graphics Laboratory — Molecular Graphics Lab". mgl.scripps.edu. Retrieved 2019-05-22.
  4. ^ "Arthur Olson | Scripps Research". www.scripps.edu. Retrieved 2019-05-22.
  5. ^ 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
  6. ^ 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.
  7. ^ "Molecules in Motion: Computer Simulations Lead to a Better Understanding of Protein Structures". www.nsf.gov. Retrieved 2019-05-22.
  8. ^ "AutoDock — AutoDock". autodock.scripps.edu. Retrieved 2019-05-22.
  9. ^ "Debian Package Tracker - autodocksuite". tracker.debian.org. Retrieved 2019-05-22.
  10. ^ "Debian Package Tracker - autodock-vina". tracker.debian.org. Retrieved 2019-05-22.
  11. ^ "Package autodocksuite". apps.fedoraproject.org. Retrieved 2019-05-22.
  12. ^ "AUR (en) - autodock-vina". aur.archlinux.org. Retrieved 2019-05-22.
  13. ^ "How to compile autodock as native 64 bit windows application — AutoDock". autodock.scripps.edu. Retrieved 2019-05-22.
  14. ^ AutoDock for GPUs using OpenCL. Contribute to ccsb-scripps/AutoDock-GPU development by creating an account on GitHub, Center for Computational Structural Biology, 2019-08-23, retrieved 2019-09-15
  15. ^ "smina". SourceForge. Retrieved 2019-09-15.
  16. ^ "Off-Target Pipeline". sites.google.com. Retrieved 2019-05-22.
  17. ^ "Consensus Scoring ToolKit | consensus scoring optimization for protein ligand docking". Retrieved 2019-05-22.
  18. ^ "Turning Docking and Virtual Screening as simple as it can get..." www.fc.up.pt. Retrieved 2019-05-22.
  19. ^ "Welcome to the PyRx Website".
  20. ^ 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.
  21. ^ "Omixon - Products - Docking". web.archive.org. 2010-03-05. Retrieved 2019-05-22.
  22. ^ Pechan, Imre. "FPGA-Based Acceleration of the AutoDock Molecular Docking Software". BME MDA, a Műegyetem Digitális Archivuma. Retrieved 2019-05-22.

External links[edit]