AMDock

"AMDock" (Assisted Molecular Docking) is a comprehensive and user-friendly graphical tool to facilitate the docking of protein-ligand complexes. It supports using AutoDock Vina and AutoDock4 for docking simulations, including a specialized option for metalloproteins through the AutoDock4Zn force field. AMDock is crafted to assist researchers, especially those new to molecular docking, by simplifying and streamlining the docking process by integrating various external programs and utilities.

Key Features and Functionalities:

- Support for AutoDock Vina and AutoDock4: AMDock allows users to perform docking studies using leading docking software, ensuring compatibility with various docking scenarios.

- AutoDock4Zn Force Field for Metalloproteins: Specialized support for docking studies involving metalloproteins, offering enhanced accuracy in these complex simulations.

- Integrated External Programs: Incorporates tools like Open Babel, PDB2PQR, AutoLigand, and ADT scripts for precise preparation of input structure files and optimal definition of the search space, allowing for tailored docking studies with varying levels of user input and supervision.

- PyMOL for Molecular Visualization: Utilizes PyMOL for visualizing molecular structures, automatically launching with predefined visualization schemes. This feature aids in setting up the docking search space and analyzing docking results.

- Off-Target Docking Procedure: Implements an off-target docking feature to facilitate ligand selectivity studies, enhancing the tool's utility in drug development and research.

- User-Friendly Graphical Interface: Designed with a focus on usability, AMDock offers a graphical interface that simplifies complex docking tasks, making molecular docking accessible to beginners.