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 Vina is available under the Apache license.
About
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 is currently maintained by The Scripps Research Institute and Olson Laboratory.
Programs
AutoDock consists of two main programs:
- AutoDock for docking of the ligand to a set of grids describing the target protein;
- AutoGrid for pre-calculating these grids.
AutoDock has an improved version, AutoDock Vina which has an improved local search routine and makes use of multicore/multi-CPU computer setups.[2]
Usage of AutoDock has contributed to the discovery of several drugs, including HIV1 integrase inhibitors.[3]
Third-party improvements
As an open source project, AutoDock has gained several third-party improved versions such as:
- GPU improved calculation routines
- SSE improved calculation routines
- Integration within bigger projects: OFF-TARGET PIPELINE https://sites.google.com/site/offtargetpipeline
- Rescoring of AutoDock Vina poses with multiple scoring functions and calibration of Consensus Scoring equations: CONSENSUS SCORING TOOLKIT http://consscortk.molsim.pharm.uoa.gr/
64 bit native compilation
Compiling the application in native 64-bit mode enables faster floating-point operation of the software.[4]
FPGA acceleration
Using general programmable chips as co-processors, speedup was within the range 10x-100x the speed of standard Intel Dual Core 2 GHz CPU.
- OMIXON experimental product. Please refer to: https://web.archive.org/web/20100305073154/http://www.omixon.com/omixon/faces/prod_docking.jsp
- Budapest University of Technology and Economics Please refer to: http://mycite.omikk.bme.hu/doc/104429.pdf
Others
- VSLAB is a VMD plug-in that allows the use of autodock directly from VMD. This program is very easy to use and allows almost anyone to dock a ligand into a protein.[5]
- 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.[6]
References
- ↑ 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.
- ↑ 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
- ↑ Schames, J.R., R.H. Henchman, J.S. Siegel, C.A. Sotriffer, H. Ni, and J.A. McCammon, Discovery of a novel binding trench in HIV integrase. J Med Chem, 2004. 47(8): 1879-81 doi:10.1021/jm0341913.
- ↑ How to compile autodock as native 64 bit windows application (sic)
- ↑ Turning Docking and Virtual Screening as simple as it can get...
- ↑ https://pyrx.sourceforge.io
- https://www.nsf.gov/discoveries/disc_summ.jsp?cntn_id=104280 Molecules in Motion: Computer Simulations Lead to a Better Understanding of Protein Structures
- Hwangseo Park; Jinuk Lee & Sangyoub Lee, Critical assessment of the automated AutoDock as a new docking tool for virtual screening