Exploring protein structures: From analysis to prediction
Understanding protein structure is key to unlocking biological function and interactions. This two-day course introduces the fundamental principles of protein structure analysis and prediction for researchers who are new to the field. You will learn how to explore, compare, and visualize protein structures and gain insights into modern prediction methods. The training also covers approaches for designing protein variants and studying protein-protein interactions, combining theory with extensive hands-on practice.
Learning outcomes
- Visualize protein structures and compare homologous proteins using ChimeraX to interpret structural similarities and differences.
- Search for structurally similar proteins using FoldSeek
- Design new stable proteins with web-based tools like PROSS or ProtFire
- Set up and execute in silico site-directed mutagenesis experiments on the VSC HPC using tools like MutateX
- Predict 3D protein structures using AlphaFold2 on the VSC HPC and analyze the quality of the resulting models
- Apply AlphaPulldown to conduct protein-protein interaction screens
- Formulate a research question involving structural prediction and select appropriate tools (e.g., AlphaFold3, Boltz-1, Chai-1) to address it
Approach
On the first day, we combine short theoretical sessions with extensive hands-on exercises. On the second day, participants will apply these protein prediction tools to their research questions, with guided support.
Required skills
- Get to know the data generated from protein structure determination experiments (high-resolution NMR spectroscopy, X-ray crystallography, electron microscopy, ...) and where to get it.
- Follow the Quick Start User guide of ChimeraX