Workshops and courses

ELIXIR node event Introduction to protein structure analysis and prediction

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Date: 8 - 9 September 2025

Language of instruction: English

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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.

Keywords: advanced bioinformatics

Venue: Ghent - VIB/UGent FSVM II, Technologiepark 75

City: Zwijnaarde

Country: Belgium

Postcode: 9052

Learning objectives:

  • 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
  • Predict 3D protein structures using AlphaFold2 on the VSC HPC and analyze the quality of the resulting models
  • 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
  • Visualize protein structures and compare homologous proteins using ChimeraX to interpret structural similarities and differences

Organizer: VIB

Event types:

  • Workshops and courses

Sponsors: Vlaams Supercomputer Centrum

Instructors: Jasper Zuallaert, Kenneth Verstraete, Alexander Botzki

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