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]
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 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]
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]
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]
^ abSchames 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. PMID15055986.
^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. PMID16988956. S2CID28351121.
^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. PMID29533817. S2CID3849603.
