AlphaFold 3 for Predicting Biomolecular Structures and Interactions

Author: Xiping Gong (xipinggong@uga.edu) Department of Crop and Soil Sciences, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA 30223, USA

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📘 Overview

You can read this Jupyter Notebook (alphafold3.ipynb) in the main directory, which is a hands-on tutorial to help you learn how to use AlphaFold 3 (AF3) to predict biomolecular structures and interactions. It provides a step-by-step workflow showing how you can use AF3 as a beginner.

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🧩 Learning Objectives

By working through this notebook, you will learn how to:

• Predict protein 3D structures from amino acid sequences using AF3.
• Predict protein–ligand complexes and explore binding interactions.
• Calculate RMSD values and visualize predicted structures using MDTraj and VMD.

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⚙️ Prerequisites and Setup

• AlphaFold 3 must be installed.
  Official GitHub: https://github.com/google-deepmind/alphafold3

• Dependencies:
  Some useful Python packages like mdtraj, openmm, and biopython need to be preinstalled.
  For additional setup help, see: https://xipinggong.com/files/tutorials/setup.html

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