AutoDockAnalyzer (ADA)

Interactive PyMOL 3 plugin for the analysis of AutoDock4 and AutoDock Vina docking results.

🧪 Description

AutoDockAnalyzer is a light and portable plugin for PyMOL designed to analyze docking results from AutoDock (.dlg) and AutoDock Vina (.pdbqt). It provides AutoDock-like clustering, thermodynamic data, and visualization tools comparable to AutoDockTools, with extended interactive capabilities.

✨ Features

• AutoDock-like clustering based on RMSD
• Interactive table (click to visualize clusters)
• Extraction of:
  • Best pose
  • Medoid (representative structure)
• Thermodynamic calculations from ΔG scoring:
  • Dissociation constant (Kd)
  • pKd (−log10 Kd)
• Cluster population visualization (bar plot)
• Table sorting (like Excel)
• Highlight selected cluster interactively
• AutoDock Vina poses visualization
• Hydrogen bond detection

📊 Output

The plugin provides:

Cluster	Size	Energy	Kd	pKd	Mean	SD

Installing the plugin

🖥️ Download the repo and extract the files. Then, in PyMOL click on Plugin -> Plugin Manager -> Install New Plugin -> Install from local file (Choose File ...) and select the init.py file in the plugin folder. You can access the plugin from the Plugin tab in PyMOL.

📄 How to cite

Garcia-Marin, J., AutoDockAnalyzer, 2026, https://github.com/reibag/AutoDockAnalyzer/