This article presents a PyMOL plugin that integrates molecular docking with visualization tools, enabling structure-based drug design. The plugin allows users to perform molecular docking using Autodock or Autodock/Vina, and to analyze binding sites and docking results within PyMOL. The plugin provides a user-friendly interface for defining binding sites, preparing receptor and ligand files, running docking simulations, and visualizing docking poses and interaction maps. It also supports the analysis and export of virtual screening results. The binding site is defined using a rectangular box, which can be set by coordinates or a PyMOL selection. The size and position of the box can be adjusted. The plugin generates necessary files for receptor and ligand definitions and allows users to select flexible residues. Docking runs can be initiated from within PyMOL, and results can be visualized and analyzed. The plugin also provides functionality to view and analyze interaction maps generated by Autodock, such as grid maps for interaction energies, which can guide ligand optimization. Docking poses can be loaded into PyMOL, and multiple poses can be analyzed simultaneously using an intuitive notebook layout. Results from multiple docking runs are summarized in a table, and the ranked list of docked ligands can be exported in various formats. The plugin is available free of charge with source code and can be obtained from the provided URL. The plugin is designed to enhance structure-based drug design by combining the visualization capabilities of PyMOL with the docking capabilities of Autodock and Autodock/Vina. It is intended for use by scientists who may not be experts in docking protocols, allowing them to perform docking studies within their preferred environment. The plugin is developed for Linux with PyMOL version 1.2 and requires MGLTools version 1.5.4 and NumPy version 1.3. While it has been reported to work on other platforms, no support is provided for them.This article presents a PyMOL plugin that integrates molecular docking with visualization tools, enabling structure-based drug design. The plugin allows users to perform molecular docking using Autodock or Autodock/Vina, and to analyze binding sites and docking results within PyMOL. The plugin provides a user-friendly interface for defining binding sites, preparing receptor and ligand files, running docking simulations, and visualizing docking poses and interaction maps. It also supports the analysis and export of virtual screening results. The binding site is defined using a rectangular box, which can be set by coordinates or a PyMOL selection. The size and position of the box can be adjusted. The plugin generates necessary files for receptor and ligand definitions and allows users to select flexible residues. Docking runs can be initiated from within PyMOL, and results can be visualized and analyzed. The plugin also provides functionality to view and analyze interaction maps generated by Autodock, such as grid maps for interaction energies, which can guide ligand optimization. Docking poses can be loaded into PyMOL, and multiple poses can be analyzed simultaneously using an intuitive notebook layout. Results from multiple docking runs are summarized in a table, and the ranked list of docked ligands can be exported in various formats. The plugin is available free of charge with source code and can be obtained from the provided URL. The plugin is designed to enhance structure-based drug design by combining the visualization capabilities of PyMOL with the docking capabilities of Autodock and Autodock/Vina. It is intended for use by scientists who may not be experts in docking protocols, allowing them to perform docking studies within their preferred environment. The plugin is developed for Linux with PyMOL version 1.2 and requires MGLTools version 1.5.4 and NumPy version 1.3. While it has been reported to work on other platforms, no support is provided for them.