DockingPie [1] is a plugin of PyMOL [2] made to fulfill the purpose of docking within the PyMOL interface. This plugin will allow you to dock using four different algorithms, namely, Vina, RxDock, SMINA, and ADFR. It will also allow you to perform flexible docking. Though the installation procedure is the same for all OSs, in this article, we are installing this plugin on Ubuntu (Linux).
Downloading the plugin
Download the zip file of DockingPie in an appropriate directory.
Installing the plugin
To install DockingPie, follow the steps mentioned below.
- Open PyMOL.
- Go to ‘Plugin Manager’ –> ‘Install New Plugin’. A new window will appear.
- Click ‘Choose’. Browse for the downloaded zip file and click ‘ok’.
- It will install the plugin. Close the window.
- Go back to the PyMOL –> ‘Plugin Manager’ –> ‘DockingPie1.2’ (DockingPie will appear in the dropdown of Plugin Manager).
Configuring the plugin
After clicking on DockingPie1.2, a new window will appear showing the four docking algorithms and a few tabs (Figure 1). You can configure it according to the docking algorithm. Scroll down and you will see different packages and a tan named ‘Install’ beneath them.
Figure 1. Screenshot of DockingPie interface showing different docking algorithms.
Download these packages and you will be able to perform docking using the DockingPie plugin in PyMOL.
References
- Rosignoli, S., & Paiardini, A. (2022). DockingPie: a consensus docking plugin for PyMOL. Bioinformatics, 38(17), 4233-4234.
- The PyMOL Molecular Graphics System, Version 2.5, Schrödinger, LLC.
