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AutoDock 作者：Garrett M. Morris 上次修改时间: 2007-09-19 16:04 Welcome!What is AutoDock? What's new? What is AutoDockTools? Where is AutoDock used? Why use AutoDock? Garrett M. Morris David S. Goodsell Ruth Huey William Lindstrom William E. Hart Scott Kurowski Scott Halliday Rik Belew Arthur J. Olson 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. AutoDock 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. 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 SoftwareMay 7, 2007 AutoDock 4 is free and now available under the GNU General Public License. Click on the "Downloads" tab. And Happy Docking! What's new?The introduction of AutoDock 4 comprises three major improvements: The docking results are more accurate and reliable. It can optionally model flexibility in the target macromolecule. 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 AutoDock 4 here. 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. We have established a mailing list for AutoDock and AutoDockTools users, autodock@scripps.edu. Here is more information about the AutoDock List (ADL) . 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 4000 academic, governmental and non-profit institutions around the world. In February of 2007, a search of the ISI Citation Index showed more than 1100 publications have cited the primary AutoDock methods papers. AutoDock is also distributed to commercial enterprises: 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. |
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