AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4
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AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4 Mario S. Valdés-Tresanco1*, Mario E. Valdés-Tresanco2,3, Pedro A. Valiente2,4 and Ernesto Moreno1*
Abstract 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. 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. 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. One particularly useful feature implemented in AMDock is the offtarget docking procedure that allows to conduct ligand selectivity studies easily. In summary, AMDock’s functional versatility makes it a very useful tool to conduct different docking studies, especially for beginners. The program is available, either for Windows or Linux, at https://github.com/Valdes-Tresanco-MS. Reviewers: This article was reviewed by Alexander Krah and Thomas Gaillard. Keywords: AMDock, AutoDock4, AutoDock Vina, AutoDock4Zn, Docking, Graphical user interface
Background Molecular docking has become a powerful tool for lead discovery and optimization. A large number of docking programs have been developed during the last three decades, based on different search algorithms and scoring functions. 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. Examples of available GUIs (developed mostly for AutoDock [1] and/or Autodock Vina [2]) are AutoDock Tools (ADT), integrated into the PMV graphical package [1], BDT [3],
Functionalities and workflow
* Correspondence: [email protected]; [email protected] 1 Faculty of Basic Sciences, University of Medellin, Medellin, Colombia Full list of author information is available at the end of the article
AMDock integrates functionalities from Autodock Vina and Autodock4, ADT scripts, AutoLigand [15], Open Babel [16], PDB2PQR [17] and PyMOL [18]. For proteins containing a zinc ion in the active site, AMDock
DOVIS [4, 5], VSDocker [6], AUDocker LE [7], WinDock [8], DockoMatic [9], PyMOL AutoDock plugin (PyMOL/AutoDock) [10], PyRx [11], MOLA [12], DockingApp [13] and JADOPPT [14]. 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 a
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