AutoDock

What is AutoDock?

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.

Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina.

AutoDock 4 actually consists of two main programs: autodock performs the docking of the ligand to a set of grids describing the target protein; autogrid pre-calculates these grids.

In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders.

AutoDock Vina does not require choosing atom types and pre-calculating grid maps for them. Instead, it calculates the grids internally, for the atom types that are needed, and it does this virtually instantly.

We have also developed a graphical user interface called AutoDockTools, or ADT for short, which amongst other things helps to set up which bonds will treated as rotatable in the ligand and to analyze dockings.

AutoDock has applications in: X-ray crystallography; structure-based drug design; lead optimization; virtual screening (HTS); combinatorial library design; protein-protein docking; chemical mechanism studies.

AutoDock 4 is free and is available under the GNU General Public License. AutoDock Vina is available under the Apache license, allowing commercial and non-commercial use and redistribution. Click on the "Downloads" tab. And Happy Docking!

What is AutoDock Vina?

AutoDock Vina is a new generation of docking software from the Molecular Graphics Lab. It achieves significant improvements in the average accuracy of the binding mode predictions, while also being up to two orders of magnitude faster than AutoDock 4.¹

Because the scoring functions used by AutoDock 4 and AutoDock Vina are different and inexact, on any given problem, either program may provide a better result.

Detailed information can be found on the AutoDock Vina web site.

What's new?

AutoDock 4.2 is faster than earlier versions, and it allows sidechains in the macromolecule to be flexible. As before, rigid docking is blindingly fast, and high-quality flexible docking can be done in around a minute. Up to 40,000 rigid dockings can be done in a day on one cpu.

AutoDock 4.2 now has a free-energy scoring function that is based on a linear regression analysis, the AMBER force field, and an even larger set of diverse protein-ligand complexes with known inhibition constants than we used in AutoDock 3.0. The best model was cross-validated with a separate set of HIV-1 protease complexes, and confirmed that the standard error is around 2.5 kcal/mol. This is enough to discriminate between leads with milli-, micro- and nano-molar inhibition constants.

You can read more about the new features in AutoDock 4.2 and how to use them in the AutoDock4.2 User Guide.

AutoDock 4 is Free Software

The introduction of AutoDock 4 comprises three major improvements:

1. The docking results are more accurate and reliable.
2. It can optionally model flexibility in the target macromolecule.
3. It enables AutoDock's use in evaluating protein-protein interactions.

AutoDock 4.0 not only is it faster than earlier versions, it allows sidechains in the macromolecule to be flexible. As before, rigid docking is blindingly fast, and high-quality flexible docking can be done in around a minute. Up to 40,000 rigid dockings can be done in a day on one cpu.

AutoDock 4.0 now has a free-energy scoring function that is based on a linear regression analysis, the AMBER force field, and an even larger set of diverse protein-ligand complexes with known inhibiton constants than we used in AutoDock 3.0. The best model was cross-validated with a separate set of HIV-1 protease complexes, and confirmed that the standard error is around 2.5 kcal/mol. This is enough to discriminate between leads with milli-, micro- and nano-molar inhibition constants.

You can read more details about the new features in AutoDock4.2 User Guide.

AutoDock 4.0 can be compiled to take advantiage of new search methods from the optimization library, ACRO, developed by William E. Hart at Sandia National Labs. We have also added some new features to our existing evolutionary methods. We still provide the Monte Carlo simulated annealing (SA) method of 2.4 and earlier. The Lamarckian Genetic Algorithm (LGA) is a big improvement on the Genetic Algorithm, and both genetic methods are much more efficient and robust than SA.

Mailing List and Forum

We have established a mailing list and forum for AutoDock users. Here is more information about the AutoDock List (ADL). URL for the forum is http://mgl.scripps.edu/forum.

What is AutoDockTools (ADT)?

We have developed and continue to improve our graphical front-end for AutoDock and AutoGrid, ADT (AutoDockTools). It runs on Linux, Mac OS X, SGI IRIX and Microsoft Windows. We also have new tutorials, along with accompanying sample files.

Where is AutoDock Used?

AutoDock has now been distributed to more than 29000 users around the world. It is being used in academic, governmental, non-profit and commercial settings. In January of 2011, a search of the ISI Citation Index showed more than 2700 publications have cited the primary AutoDock methods papers.

AutoDock is now distributed under the GPL open source license and is freely available for all to use. Because of the restrictions of incorporating GPL licensed software into other codes for the purpose of redistribution, some companies may wish to license AutoDock under a separate license agreement - which we can arrange. Please contact Prof. Arthur J. Olson at + 1 (858) 784-2526 for more information.

Why Use AutoDock?

AutoDock has been widely-used and there are many examples of its successful application in the literature (see References); in 2006, AutoDock was the most cited docking software. It is very fast, provides high quality predictions of ligand conformations, and good correlations between predicted inhibition constants and experimental ones. AutoDock has also been shown to be useful in blind docking, where the location of the binding site is not known. Plus, AutoDock is free software and version 4 is distributed under the GNU General Public License; it easy to obtain, too.

Run Your AutoDock Research Project on World Community Grid!

Does your research run on AutoDock? If so, you may be eligible to benefit from World Community Grid’s free computational power to accelerate your research. AutoDock has already been “grid-enabled” by World Community Grid’s technical team and is currently being run on World Community Grid with the FightAIDS@Home project from The Scripps Research Institute and the Discover Dengue Drugs - Together project from The University of Texas Medical Branch. Please review World Community Grid’s research project criteria and contact World Community Grid if you have an idea for a project proposal or any questions.

Sumber : http://autodock.scripps.edu/