AutoDock Tutorial

This tutorial provides a structured introduction to molecular docking using AutoDock Vina, with emphasis on the theoretical and practical principles underlying ligand–receptor binding analysis. It guides users through the preparation of molecular input files, definition of docking parameters, execution of docking simulations, and interpretation of predicted binding modes and affinity estimates. The tutorial is intended as a pedagogical resource for the development of foundational competencies in docking-based computational analysis. For a more comprehensive treatment of the subject, readers are encouraged to consult specialized literature and additional online resources.

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Contents:

Part 1. Introduction

Part 2. Protocol

1. Selection of Structures (receptor and ligand)
2. Preparation of Structures
3. Docking Setup and Execution
4. Analysis of Results

Part 3: Practical Exercises

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Downloads

• Tutorial PDF. This is the most up-to-date version of the tutorial and may continue to receive minor revisions, including the correction of typographical errors and other small improvements.

Assessment Notebooks

To complete the training and obtain credit, participants are required to engage with the tutorial materials in the prescribed sequence and to complete the two mandatory assessment notebooks:

• PDB Structure Preparation
• Receptor Reconstruction

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License & Attribution

The content of this tutorial itself is licensed under the terms and conditions of the Creative Commons Attribution (CC BY 4.0) license, and the underlying source code used to format and display that content is licensed under the MIT license. See the LICENSE files for full details.

If you use or adapt this material, please provide appropriate credit to the original authors, ACM and FFCT, as well as to the repository.

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Version 1.0 — February 2026 Back to Main Site