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AutoDock

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(Redirected from Smina)
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 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 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

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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

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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

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AutoDock for GPUs

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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

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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

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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

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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

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References

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  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. ^ a b 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. ^ a b 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. ^ a b 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. ^ 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. 29 July 2005. 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. ^ 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. PMC 10683950. 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. BME MDA, a Műegyetem Digitális Archivuma. ISBN 9783981375411. Retrieved 2019-05-22.
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