MGLTools Unless otherwise stated, packages that do not specify a license are released under the MOZILLA Open Source License. Check the licenses! Thew MGLTools software suite was developed in the Sanner lab at the Center for Computational Structural Biology (CCRB) formerly known as the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures. Navigation portlet on the left has links to downloads, screenshots, documentation section of this website where you can find more information about MGLTools. MGLTools comprises: the Python Molecular Viewer (PMV), a general purpose molecular viewer AutoDockTools (ADT) a set of PMV commands specifically developed to support AutoDock users Vision, a visual programing environment. MSMS - binaries of the MSMS C library. This allows you to run msms as a standalone application. A wrapped version of the library comes with MGLTools. The MGLTools uses the MSLIB package to compute molecular surfaces. AutoDock AutoDock 4 is free and is available under the GNU General Public License. AutoDock is a Command-line interface 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 Vina AutoDock Vina is released under a very permissive Apache license, with few restrictions on commercial or non-commercial use, or on the derivative works AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute. AutoDockTools AutoDockTools, or ADT, is the free GUI for AutoDock developed by the same laboratory that develops AutoDock. You can use it to set up, run and analyze AutoDock dockings and isocontour AutoGrid affinity maps, as well as compute molecular surfaces, display secondary structure ribbons, compute hydrogen-bonds, and do many more useful things. AutoDockTools, or ADT, is the ultimate GUI to set up, launch and analyze AutoDockruns. With ADT, you can: View molecules in 3D, rotate & scale in real time. Add all hydrogens or just non-polar hydrogens. Assign partial atomic charges to the ligand and the macromolecule (Gasteiger or Kollman United Atom charges). Merge non-polar hydrogens and their charges with their parent carbon atom. Set up rotatable bonds in the ligand using a graphical version of AutoTors. Set up the AutoGrid Parameter File (GPF) using a visual representation of the grid box, and slider-based widgets. Set up the AutoDock Parameter File (DPF) using forms. Launch AutoGrid and AutoDock. Read in the results of an AutoDock job and graphically display them. View isocontoured AutoGrid affinity maps.