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.
For questions, support, and discussions, subscribe to the AutoDock mailing list. It should be noted that all six of the other docking programs, to which it was compared, are distributed commercially. Binding mode prediction accuracy on the test set. Ease of Use.
All that is required is the structures of the molecules being docked and the specification of the search space including the binding site. Calculating grid maps and assigning atom charges is not needed. The summary automatically remains in sync with the possible usage scenarios. Like in AutoDock 4, some receptor side chains can be chosen to be treated as flexible during docking. AutoDock Vina tends to be faster than AutoDock 4 by orders of magnitude. Some of these projects average over 50 years worth of computation per day.
AutoDockFR is a computational docking program with flexible protein targets, including sidechain motion and induced fit. AutoDockCrankPep is a program for computational docking of peptides to protein targets. It is freely available on PubMedCentral, and also available in nice formatted form through Nature Protocols. Be sure to download the supplementary files, which include several worked examples that you can try out.
This tutorial will introduce you to three programs with the core functionality of AutoDock:. Several specialized docking programs are available as you become more familiar with docking and encounter systems that require special treatment. These include:. If you are interested in virtual screening, Raccoon2 provides a dedicated graphical user interface for managing coordinates and docking, and analyzing results.
We have also created specialized tools for different aspects of docking preparation and analysis, such as the binding site prediction software AutoSite and AutoLigand. It brings together a community of people that have common interests in molecular modeling software related to docking and AutoDock, and are here for learning or helping others. It is also a forum for suggesting new features, and new software versions and functionality will be announced on the list.
Documentation, tutorials, download instructions, and other useful information is available at the sites for each software.
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