Install AUTODOCK in Windows Installing AUTODOCK software in WINDOWS operating system. Does not help at all. For windows 10 is it the same procedure? Reply Delete. Saurabh Srivastava April 11, 2017 at 5:49 AM. This comment has been removed by the author. Reply Delete. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. To install AutoDock, download the Windows installer (download page) and run it. By default, the programs will be installed in the Program Files directory (i.e. C:Program FilesThe Scripps Research InstituteAutodock). AutoDock 4.2.6:: DESCRIPTION. AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock is now distributed freely under the GNU GPL for all to use. If you plan to use AutoDock for commercial purposes we encourage donations to the Olson Laboratory to help support further development of the AutoDock suite of programs. Please make out any donations checks to. What is WCGridAutoDock.exe? The.exe extension on a filename indicates an exe cutable file. Executable files may, in some cases, harm your computer. Therefore, please read below to decide for yourself whether the WCGridAutoDock.exe on your computer is a Trojan that you should remove, or whether it is a file belonging to the Windows operating system or to a trusted application.
Developer(s) | The Scripps Research Institute |
---|---|
Initial release | 1989; 30 years ago |
Stable release | 4.2.6 (AutoDock), 1.1.2 (AutoDock Vina) / 2014; 5 years ago (AutoDock), 2011; 8 years ago (AutoDock Vina) |
Written in | C++, C |
Operating system | Linux, Mac OS X, SGI IRIX, and Microsoft Windows |
Platform | Many |
Available in | English |
Type | Protein–ligand docking |
License | GPL (AutoDock), Apache License (AutoDock Vina) |
Website | autodock.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]
- 3Improved versions
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]
Autodock 4
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]
- ^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. ISSN0887-3585. PMID16862531.
- ^ abTrott, 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, PMC3041641, PMID19499576
- ^'The Molecular Graphics Laboratory — Molecular Graphics Lab'. mgl.scripps.edu. Retrieved 2019-05-22.
- ^'Arthur Olson | Scripps Research'. www.scripps.edu. Retrieved 2019-05-22.
- ^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, PMID16988956
- ^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. ISSN0022-2623. PMID15055986.
- ^'Molecules in Motion: Computer Simulations Lead to a Better Understanding of Protein Structures'. www.nsf.gov. Retrieved 2019-05-22.
- ^'AutoDock — AutoDock'. autodock.scripps.edu. Retrieved 2019-05-22.
- ^'Debian Package Tracker - autodocksuite'. tracker.debian.org. Retrieved 2019-05-22.
- ^'Debian Package Tracker - autodock-vina'. tracker.debian.org. Retrieved 2019-05-22.
- ^'Package autodocksuite'. apps.fedoraproject.org. Retrieved 2019-05-22.
- ^'AUR (en) - autodock-vina'. aur.archlinux.org. Retrieved 2019-05-22.
- ^'How to compile autodock as native 64 bit windows application — AutoDock'. autodock.scripps.edu. Retrieved 2019-05-22.
- ^GitHub - ccsb-scripps/AutoDock-GPU: AutoDock for GPUs using OpenCL., Center for Computational Structural Biology, 2019-08-23, retrieved 2019-09-15
- ^'smina'. SourceForge. Retrieved 2019-09-15.
- ^'Off-Target Pipeline'. sites.google.com. Retrieved 2019-05-22.
- ^'Consensus Scoring ToolKit | consensus scoring optimization for protein ligand docking'. Retrieved 2019-05-22.
- ^'Turning Docking and Virtual Screening as simple as it can get...'www.fc.up.pt. Retrieved 2019-05-22.
- ^'Welcome to the PyRx Website'.
- ^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. PMID29533817.
- ^'Omixon - Products - Docking'. web.archive.org. 2010-03-05. Retrieved 2019-05-22.
- ^Pechan, Imre. 'FPGA-Based Acceleration of the AutoDock Molecular Docking Software'. BME MDA, a Műegyetem Digitális Archivuma. Retrieved 2019-05-22.
External links[edit]
Retrieved from 'https://en.wikipedia.org/w/index.php?title=AutoDock&oldid=918019677'