Introduction to Protein Structure Analysis and Prediction - September 2023
Introduction to Protein Structure Analysis and Prediction - September 2023
04 sep
05 sep
General context
This two-day training session will provide the basics of protein structure analysis and how this information is stored in databases.
On the two days, we will explore and search in online databases containing protein structure information including models from AlphaFoldDB. Furthermore, we will visualize protein structures using Chimera. Different hands-on exercises will allow you to compare the structure of homologues. We will use (online) tools to quantify various interactions in the structures.
We will use AlphaFold2 via the HPC cluster at the VSC UGhent to predict structural models of proteins. An overview of different protein folding predictors is discussed, such as ESMFold, OpenFold and RoseTTaFold.
In the afternoon, the second day is dedicated to your own research question you might want to address via structural predictions using AlphaFold2. Additionally, we will learn to use AlphaPulldown, a Python package that streamlines protein-protein interaction screens.
Day 1:
- 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.
- Display protein structure data and compare structures, through the use of Chimera.
- Create high-quality graphical representations of the structures.
Day 2:
- Introduction to AlphaFold2 and the technical setup at the VSC
- Predict three-dimensional protein models with AlphaFold2 using the HPC at the VSC UGhent
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Dive in your research question where structural prediction via AlphaFold will be used.
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A broader perspective on other protein folding predictors (ESMFold, OpenFold, RoseTTaFold)
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This part is cancelled due to installation issues on the HPC.
Use AlphaPulldown to execute protein-protein interaction screens using AlphaFold
You are encouraged to use your own laptop.
Chimera
AlphaFold2
AlphaPulldown (cancelled)
Trainers
Alexander Botzki
Alexander Botzki is heading the Technology training unit at VIB, the Flemish Institute of Biotechnology, Belgium. The main mission of this unit is 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'.
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.
Program
Exploring the Protein Data Bank and related databases.
Assessing the quality of a structure and the information that can be derived from it
Visualizing protein structures (Chimera)
Comparing structures
Predict structural models of proteins using AlphaFold2 via the HPC cluster
Use AlphaPullDown for protein-protein interaction screening
Own research questions
Practical info
04 September 2023 - 05 September 2023
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
04 September 2023 - 05 September 2023
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take bus 49, 50 or 70 to Technologiepark. Please check Routeplanner De Lijn for schedules.
04 September 2023 - 05 September 2023
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket and have it validated at the reception desk of the FSVM building. Parking will only be allowed in regular parking spots (for instance in front of the building) and in the new parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited and after initial warnings, fines will be issued (€ 50).
04 September 2023 - 05 September 2023
Ghent - VIB/UGent FSVM II
Course venue: L4