AutoDock

{{Infobox software

| name = AutoDock and AutoDock Vina

| logo = AutoDock logo.jpg

| screenshot =

| caption =

| author =

| developer = Scripps Research

| released = {{Start date and age|1989}}

| latest release version = 4.2.6 (AutoDock), 1.2.0 (AutoDock Vina)

| latest release date = {{Start date and age|2014}} (AutoDock), {{Start date and age|2021}} (AutoDock Vina)

| programming language = C++, C

| operating system = Linux, Mac OS X, SGI IRIX, and Microsoft Windows

| platform = Many

| size =

| language = English

| genre = Protein–ligand docking

| license = GPL (AutoDock), Apache License (AutoDock Vina)

| website = {{URL|https://autodock.scripps.edu/}} (AutoDock) {{URL|https://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.{{cite journal | vauthors = Sousa SF, Fernandes PA, Ramos MJ | title = Protein-ligand docking: current status and future challenges | journal = Proteins | volume = 65 | issue = 1 | pages = 15–26 | date = October 2006 | pmid = 16862531 | doi = 10.1002/prot.21082 | s2cid = 21569704 }} 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.{{Cite web|url=https://www.ibm.org/OpenPandemics|title=We want to stop pandemics in their tracks. | date=2020-04-01|website=IBM|access-date=2020-04-04}} 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.{{cite journal | vauthors = Trott O, Olson AJ | title = AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading | journal = Journal of Computational Chemistry | volume = 31 | issue = 2 | pages = 455–61 | date = January 2010 | pmid = 19499576 | pmc = 3041641 | doi = 10.1002/jcc.21334 }} 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{{Cite web|title=The Center for Computational Structural Biology|url=https://ccsb.scripps.edu/ | date=2020-05-15|website=The Center for Computational Structural Biology|access-date=2020-05-15}}{{Cite web|url=https://www.scripps.edu/faculty/olson/|title=Arthur Olson {{!}} Scripps Research|website=www.scripps.edu|access-date=2019-05-22}}

AutoDock is widely used and played a role in the development of the first clinically approved HIV-1 integrase inhibitor by Merck & Co.{{cite journal | vauthors = Goodsell DS, Sanner MF, Olson AJ, Forli S | title = The AutoDock suite at 30 | journal = Protein Science | date = August 2020 | volume = 30 | issue = 1 | pages = 31–43 | pmid = 32808340 | doi = 10.1002/pro.3934 | pmc = 7737764 }}{{cite journal | vauthors = Schames JR, Henchman RH, Siegel JS, Sotriffer CA, Ni H, McCammon JA | title = Discovery of a novel binding trench in HIV integrase | journal = Journal of Medicinal Chemistry | volume = 47 | issue = 8 | pages = 1879–81 | date = April 2004 | pmid = 15055986 | doi = 10.1021/jm0341913 }}

Programs

AutoDock consists of two main programs:{{cite journal | vauthors = Park H, Lee J, Lee S | title = Critical assessment of the automated AutoDock as a new docking tool for virtual screening | journal = Proteins | volume = 65 | issue = 3 | pages = 549–54 | date = November 2006 | pmid = 16988956 | doi = 10.1002/prot.21183 | s2cid = 28351121 }}

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.{{Cite web| vauthors = Gupta G |date=2020-05-26|title=Racing the Clock, COVID Killer Sought Among a Billion Molecules|url=https://blogs.nvidia.com/blog/2020/05/26/covid-autodock-summit-ornl/|url-status=live|archive-url=https://web.archive.org/web/20200611183756/https://blogs.nvidia.com/blog/2020/05/26/covid-autodock-summit-ornl/ |archive-date=2020-06-11 |access-date=2020-09-26|website=Nvidia}}{{Cite web|url=https://www.nsf.gov/discoveries/disc_summ.jsp?cntn_id=104280|title=Molecules in Motion: Computer Simulations Lead to a Better Understanding of Protein Structures|website=www.nsf.gov|date=29 July 2005 |language=English|access-date=2019-05-22}}

Platform support

AutoDock runs on Linux, Mac OS X, SGI IRIX, and Microsoft Windows.{{Cite web|url=http://autodock.scripps.edu/|title=AutoDock — AutoDock|website=autodock.scripps.edu|access-date=2019-05-22}} It is available as a package in several Linux distributions, including Debian,{{Cite web|url=https://tracker.debian.org/pkg/autodocksuite|title=Debian Package Tracker - autodocksuite|website=tracker.debian.org|access-date=2019-05-22}}{{Cite web|url=https://tracker.debian.org/pkg/autodock-vina|title=Debian Package Tracker - autodock-vina|website=tracker.debian.org|access-date=2019-05-22}} Fedora,{{Cite web|url=https://apps.fedoraproject.org/packages/autodocksuite|title=Package autodocksuite|website=apps.fedoraproject.org|access-date=2019-05-22|archive-date=2020-01-01|archive-url=https://web.archive.org/web/20200101212814/https://apps.fedoraproject.org/packages/autodocksuite|url-status=dead}} and Arch Linux.{{Cite web|url=https://aur.archlinux.org/packages/autodock-vina|title=AUR (en) - autodock-vina|website=aur.archlinux.org|access-date=2019-05-22}}

Compiling the application in native 64-bit mode on Microsoft Windows enables faster floating-point operation of the software.{{Cite web|url=http://autodock.scripps.edu/faqs-help/how-to/how-to-compile-autodock-as-native-64-bit-windows-application|title=How to compile autodock as native 64 bit windows application — AutoDock|website=autodock.scripps.edu|access-date=2019-05-22}}

Improved versions

= AutoDock for GPUs =

Improved calculation routines using OpenCL and CUDA have been developed by the AutoDock Scripps research team.{{Citation|title=GitHub - ccsb-scripps/AutoDock-GPU: AutoDock for GPUs using OpenCL.|date=2019-08-23|url=https://github.com/ccsb-scripps/AutoDock-GPU|publisher=Center for Computational Structural Biology|access-date=2019-09-15}}

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 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.

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.{{Cite web|url=https://www.worldcommunitygrid.org/forums/wcg/viewthread_thread,41920_offset,0|title=Windows 10 or Linux | date=2019-10-31|website=World Community Grid|access-date=2020-04-04}}

AutoDock Vina is currently on version 1.2, released in July 2021.{{Citation|title=ccsb-scripps/AutoDock-Vina|date=2021-07-20|url=https://github.com/ccsb-scripps/AutoDock-Vina|publisher=Center for Computational Structural Biology|access-date=2021-07-20}}{{Cite journal|last1=Eberhardt|first1=Jerome|last2=Santos-Martins|first2=Diogo|last3=Tillack|first3=Andreas F.|last4=Forli|first4=Stefano|date=2021-07-19|title=AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings|journal=Journal of Chemical Information and Modeling|volume=61|issue=8|pages=3891–3898|doi=10.1021/acs.jcim.1c00203|pmid=34278794|issn=1549-9596|doi-access=|pmc=10683950}}

=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.{{Cite web|url=https://sourceforge.net/projects/smina/|title=smina|website=SourceForge|language=en|access-date=2019-09-15}}
Off-Target Pipeline allows integration of AutoDock within bigger projects.{{Cite web|url=https://sites.google.com/site/offtargetpipeline/|title=Off-Target Pipeline|website=sites.google.com|access-date=2019-05-22}}
Consensus Scoring ToolKit provides rescoring of AutoDock Vina poses with multiple scoring functions and calibration of consensus scoring equations.{{Cite web|url=http://consscortk.molsim.pharm.uoa.gr/|title=Consensus Scoring ToolKit {{!}} consensus scoring optimization for protein ligand docking|language=en-US|access-date=2019-05-22}}
VSLAB is a VMD plug-in that allows the use of AutoDock directly from VMD.{{Cite web|url=https://www.fc.up.pt/pessoas/nscerque/vsLab/vLab/HomePage.html|title=Turning Docking and Virtual Screening as simple as it can get...|website=www.fc.up.pt|access-date=2019-05-22}}
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.{{Cite web|url=https://pyrx.sourceforge.io/|title=Welcome to the PyRx Website}}
POAP is a shell-script-based tool which automates AutoDock for virtual screening from ligand preparation to post docking analysis.{{cite journal | vauthors = Samdani A, Vetrivel U | title = POAP: A GNU parallel based multithreaded pipeline of open babel and AutoDock suite for boosted high throughput virtual screening | journal = Computational Biology and Chemistry | volume = 74 | pages = 39–48 | date = June 2018 | pmid = 29533817 | doi = 10.1016/j.compbiolchem.2018.02.012 | s2cid = 3849603 }}
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.{{cite journal | vauthors = Gorgulla C, Boeszoermenyi A, Wang ZF, Fischer PD, Coote PW, Padmanabha Das KM, Malets YS, Radchenko DS, Moroz YS, Scott DA, Fackeldey K, Hoffmann M, Iavniuk I, Wagner G, Arthanari H | display-authors = 6 | title = An open-source drug discovery platform enables ultra-large virtual screens | journal = Nature | volume = 580 | issue = 7805 | pages = 663–668 | date = April 2020 | pmid = 32152607 | doi = 10.1038/s41586-020-2117-z | s2cid = 212653203 | bibcode = 2020Natur.580..663G | pmc = 8352709 }}

=FPGA acceleration=

Using general programmable chips as co-processors, specifically the OMIXON experimental product,{{Cite web|url=http://www.omixon.com/omixon/faces/prod_docking.jsp|archive-url=https://web.archive.org/web/20100305073154/http://www.omixon.com/omixon/faces/prod_docking.jsp|url-status=dead|archive-date=2010-03-05|title=Omixon - Products - Docking|date=2010-03-05|access-date=2019-05-22}} speedup was within the range 10x-100x the speed of standard Intel Dual Core 2 GHz CPU.{{Cite book|url=https://repozitorium.omikk.bme.hu/handle/10890/4340|title=FPGA-Based Acceleration of the AutoDock Molecular Docking Software| vauthors = Pechan I |date=|publisher=BME MDA, a Műegyetem Digitális Archivuma|isbn=9783981375411|access-date=2019-05-22}}