Examples of available GUIs (developed mostly for AutoDock and/or Autodock Vina ) are AutoDock Tools (ADT), integrated into the PMV graphical package, BDT, DOVIS, VSDocker, AUDocker LE, WinDock, DockoMatic, PyMOL AutoDock plugin (PyMOL/AutoDock), PyRx, MOLA, DockingApp and JADOPPT. Aiming to make these docking programs more user-friendly, especially to beginners, different graphical user interfaces (GUIs) have been developed to assist in the preparation of molecular systems, the execution of the calculations and/or the analysis of the results. A large number of docking programs have been developed during the last three decades, based on different search algorithms and scoring functions. Molecular docking has become a powerful tool for lead discovery and optimization.
This article was reviewed by Alexander Krah and Thomas Gaillard.
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The program is available, either for Windows or Linux, at. In summary, AMDock’s functional versatility makes it a very useful tool to conduct different docking studies, especially for beginners. One particularly useful feature implemented in AMDock is the off-target docking procedure that allows to conduct ligand selectivity studies easily. For visualization of molecular structures, AMDock uses PyMOL, starting it automatically with several predefined visualization schemes to aid in setting up the box defining the search space and to visualize and analyze the docking results.
AMDock integrates several external programs (Open Babel, PDB2PQR, AutoLigand, ADT scripts) to accurately prepare the input structure files and to optimally define the search space, offering several alternatives and different degrees of user supervision. AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4, including the option of using the Autodock4Zn force field for metalloproteins.
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