Introduction to protein structure analysis and prediction
Introduction to protein structure analysis and prediction
8 September 2025
9 September 2025
General context
Understanding protein structure is essential for researchers in molecular biology, bioinformatics, and structural biology, as it underpins insights into function, interaction, and disease mechanisms. This two-day training is designed for early-career researchers, PhD students, and postdocs who are new to protein structure analysis.
Participants will gain hands-on experience with key tools and databases, including ChimeraX, AlphaFoldDB, MutateX, and PROSS. They will use these tools to visualize, explore, and compare protein structures, and to design new ones.
The course also introduces structure prediction methods using both online platforms (AlphaFold3, Chai-1) and our local VSC infrastructure (AlphaFold2, Boltz-1). Furthermore, we will use AlphaPulldown, a Python package that streamlines protein-protein interaction screens.
On the second day, participants will apply these tools to their research questions, with guided support. By the end of the training, attendees will be equipped to independently access, analyze, and interpret protein structural data using state-of-the-art resources.
- Visualize protein structures and compare homologous proteins using ChimeraX to interpret structural similarities and differences.
- Search for structurally similar proteins using FoldSeek and evaluate the relevance of retrieved models.
- Set up and execute in silico site-directed mutagenesis experiments on the VSC HPC using tools like MutateX or PROSS.
- 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 and interpret the predicted complexes.
- Formulate a research question involving structural prediction and select appropriate tools (e.g., AlphaFold3, Boltz-1, Chai-1) to address it.
You are encouraged to use your own laptop during the hands-on session. You will need a VSC account to follow this training session efficiently. This VSC account will need to be requested at least two weeks before the training session.
- 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 https://www.rbvi.ucsf.edu/chimerax/docs/quickstart/index.html
ChimeraX
MutateX
PROSS
AlphaFold2
AlphaPulldown
AlphaFold3
Chai-1
Boltz-1
Trainers
Jasper Zuallaert
Jasper Zuallaert is a postdoctoral scientist at VIB-CMB, studying deep learning applied to protein data.
Kenneth Verstraete
Kenneth Verstraete is a structural biologist at the VIB-IRC, studying protein complexes central to immunity and metabolism.
Alexander Botzki
Alexander Botzki at the Flemish Institute of Biotechnology, Belgium has with his group the mission of providing technology training in domains of VIB Technologies, Bioinformatics & AI, Software Development, and Research Data Management. Between 2014 and 2022, he was head of the VIB Bioinformatics Core. From September 2009 to July 2014, he was responsible for the roll-out of E-Notebook (electronic lab notebook) to VIB's researchers within 75 research groups.
Before joining VIB, Alexander worked on various computational biology projects for Algonomics (bought by Lonza, 2008-2009) and DevGen (now Syngenta, from 2006-2008). During Alexander's PostDoc at Sanofi Aventis in Strasbourg, he executed various virtual screening campaigns on the compound selection of the merged enterprise. He received his doctoral degree with the group of Prof. Dr. Armin Buschauer (University of Regensburg, Germany) on 'Structure-based design of hyaluronidase inhibitors'.
Program
9:30 Introduction to Protein Structure Analysis
Assessing the quality of a structure and the information that can be derived from it
Visualizing protein structures and Comparing structures (ChimeraX)
FoldSeek - finding distantly related 3D structures
PROSS - investigate stable protein variants online
MutateX - automated computational mutagenesis analysis
17:00 End of the day
09:30 Predict structural models of proteins using AlphaFold2 via the HPC cluster
Use AlphaPullDown for protein-protein interaction screening
Own research questions
17:00 End of the day
Practical info
08 September 2025 - 09 September 2025
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
08 September 2025 - 09 September 2025
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
08 September 2025 - 09 September 2025
Ghent - VIB/UGent FSVM II
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
08 September 2025 - 09 September 2025
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.
08 September 2025 - 09 September 2025
Ghent - VIB/UGent FSVM II
Room L4 (4th floor)