Software:AutoDock

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AutoDock and AutoDock Vina
AutoDock logo.jpg
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

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. ↑ "Protein-ligand docking: current status and future challenges". Proteins 65 (1): 15–26. October 2006. doi:10.1002/prot.21082. PMID 16862531. 
  2. ↑ "We want to stop pandemics in their tracks.". 2020-04-01. https://www.ibm.org/OpenPandemics. 
  3. ↑ 3.0 3.1 "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. January 2010. doi:10.1002/jcc.21334. PMID 19499576. 
  4. ↑ "The Center for Computational Structural Biology". 2020-05-15. https://ccsb.scripps.edu/. 
  5. ↑ "Arthur Olson | Scripps Research". https://www.scripps.edu/faculty/olson/. 
  6. ↑ 6.0 6.1 "The AutoDock suite at 30". Protein Science 30 (1): 31–43. August 2020. doi:10.1002/pro.3934. PMID 32808340. 
  7. ↑ 7.0 7.1 "Discovery of a novel binding trench in HIV integrase". Journal of Medicinal Chemistry 47 (8): 1879–81. April 2004. doi:10.1021/jm0341913. PMID 15055986. 
  8. ↑ "Critical assessment of the automated AutoDock as a new docking tool for virtual screening". Proteins 65 (3): 549–54. November 2006. doi:10.1002/prot.21183. PMID 16988956. 
  9. ↑ 9.0 9.1 "Racing the Clock, COVID Killer Sought Among a Billion Molecules". 2020-05-26. https://blogs.nvidia.com/blog/2020/05/26/covid-autodock-summit-ornl/. 
  10. ↑ "Molecules in Motion: Computer Simulations Lead to a Better Understanding of Protein Structures" (in English). https://www.nsf.gov/discoveries/disc_summ.jsp?cntn_id=104280. 
  11. ↑ "AutoDock — AutoDock". http://autodock.scripps.edu/. 
  12. ↑ "Debian Package Tracker - autodocksuite". https://tracker.debian.org/pkg/autodocksuite. 
  13. ↑ "Debian Package Tracker - autodock-vina". https://tracker.debian.org/pkg/autodock-vina. 
  14. ↑ "Package autodocksuite". https://apps.fedoraproject.org/packages/autodocksuite. 
  15. ↑ "AUR (en) - autodock-vina". https://aur.archlinux.org/packages/autodock-vina. 
  16. ↑ "How to compile autodock as native 64 bit windows application — AutoDock". http://autodock.scripps.edu/faqs-help/how-to/how-to-compile-autodock-as-native-64-bit-windows-application. 
  17. ↑ 17.0 17.1 GitHub - ccsb-scripps/AutoDock-GPU: AutoDock for GPUs using OpenCL., Center for Computational Structural Biology, 2019-08-23, https://github.com/ccsb-scripps/AutoDock-GPU, retrieved 2019-09-15 
  18. ↑ "Windows 10 or Linux". 2019-10-31. https://www.worldcommunitygrid.org/forums/wcg/viewthread_thread,41920_offset,0. 
  19. ↑ ccsb-scripps/AutoDock-Vina, Center for Computational Structural Biology, 2021-07-20, https://github.com/ccsb-scripps/AutoDock-Vina, 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" (in en). https://sourceforge.net/projects/smina/. 
  22. ↑ "Off-Target Pipeline". https://sites.google.com/site/offtargetpipeline/. 
  23. ↑ "Consensus Scoring ToolKit | consensus scoring optimization for protein ligand docking" (in en-US). http://consscortk.molsim.pharm.uoa.gr/. 
  24. ↑ "Turning Docking and Virtual Screening as simple as it can get...". https://www.fc.up.pt/pessoas/nscerque/vsLab/vLab/HomePage.html. 
  25. ↑ "Welcome to the PyRx Website". https://pyrx.sourceforge.io/. 
  26. ↑ "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. June 2018. doi:10.1016/j.compbiolchem.2018.02.012. PMID 29533817. 
  27. ↑ "An open-source drug discovery platform enables ultra-large virtual screens". Nature 580 (7805): 663–668. April 2020. doi:10.1038/s41586-020-2117-z. PMID 32152607. Bibcode: 2020Natur.580..663G. 
  28. ↑ "Omixon - Products - Docking". 2010-03-05. http://www.omixon.com/omixon/faces/prod_docking.jsp. 
  29. ↑ FPGA-Based Acceleration of the AutoDock Molecular Docking Software. BME MDA, a Műegyetem Digitális Archivuma. ISBN 9783981375411. https://repozitorium.omikk.bme.hu/handle/10890/4340. Retrieved 2019-05-22. 

External links



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