![]() The AMDock main window has five tabs: 1) Home, 2) Docking Options, 3) Results Analysis, 4) Configuration, and 5) Info. On Linux, only Open Babel and PyMOL should be installed (both tools are included in most popular Linux repositories). ![]() On Windows, it is packaged together with all the integrated tools, hence no additional software installation is required. AMDock is coded in Python 2.7 and is available for Windows and Linux. For proteins containing a zinc ion in the active site, AMDock has the option of using the specially tailored Autodock4Zn parameters. Functionalities and workflowĪMDock integrates functionalities from Autodock Vina and Autodock4, ADT scripts, AutoLigand, Open Babel, PDB2PQR and PyMOL. We present here a new multi-platform tool, AMDock (Assisted Molecular Docking), whose main advantage over its predecessors is the integration of several valuable external tools within a simple and intuitive graphical interface that guides the users along well-established docking protocols - using either Autodock4 or AutoDock Vina - from system preparation to analysis of results. 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. 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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