Class lab activity; Protein-ligand docking Analysis with AlphaFold - AP/Uni Lab Tutorial

Описание: This tutorial walks instructors through a bioinformatics lab activity designed for AP Biology and introductory undergraduate biology courses. In this lab, students use AlphaFold to generate a predicted 3D structure of the Epidermal Growth Factor Receptor (EGFR) and compare it to an experimentally validated structure obtained from the Protein Data Bank (PDB).

This activity introduces students to real-world computational biology and allows them to critically evaluate AI-generated models versus experimentally determined protein structures. The lab reinforces structure–function relationships while integrating modern tools used in drug discovery and cancer research.

In this tutorial, instructors will learn how to guide students through:

1. Retrieving amino acid sequences and 3D protein structures from the Protein Data Bank (PDB)
2. Generating a predicted protein structure using AlphaFold
3. Understanding common structural biology file formats (PDB, CIF, etc.)
4. Preparing an experimental protein structure by removing bound ligands
5. Identifying potential binding pockets within a protein
6. Performing molecular docking to evaluate protein–ligand interactions
7. Retrieving small molecule ligand data from PubChem
8. Comparing predicted vs experimental structures to analyze structural accuracy

This lab supports instruction in:

Structure determines function
Protein folding and R-group interactions
Applications of AI in modern science
Computational approaches to drug discovery
Critical evaluation of scientific models

This activity is ideal for instructors looking to incorporate AI, bioinformatics, and authentic research practices into the AP Biology macromolecules unit or introductory undergraduate molecular biology courses.

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