Exploring protein structures: From analysis to prediction
Exploring protein structures: From analysis to prediction
25 November 2026, 09h30 - 17h00
26 November 2026, 09h30 - 17h00
General context
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.
- 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
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.
- 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
- ChimeraX
- Foldseek
- PROSS or FireProt
- MutateX
- AlphaFold2
- AlphaPulldown
- AlphaFold3
- Chai-1
- Boltz-1
This course is part of the learning path Structural biology.
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. You will need to request this VSC account at least two weeks before the training session.
AI methods used
This course uses advanced AI-based structure prediction methods such as AlphaFold and related tools to infer three-dimensional protein structures and protein–protein interactions from sequence data. These approaches rely on deep learning models trained on large structural datasets to capture complex sequence–structure relationships.
Trainers
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'.
Kenneth Verstraete
Kenneth Verstraete is a structural biologist at the VIB-IRC, studying protein complexes central to immunity and metabolism.
Jasper Zuallaert
Jasper Zuallaert is a postdoctoral scientist at VIB-CMB, studying deep learning applied to protein data.
Program
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 mutagenesis analysis
Wrap up
Predict structural models of protrein using AlphaFold2 via the HPC cluster
Use AlphaPullDown for protein-protein interaction screening
Own research questions
Wrap-up
Practical info
25 November 2026 - 26 November 2026
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
25 November 2026 - 26 November 2026
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
25 November 2026 - 26 November 2026
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.
25 November 2026 - 26 November 2026
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.