Introduction to Protein Structure Analysis and Prediction - September 2024 (Ghent)
Introduction to Protein Structure Analysis and Prediction - September 2024 (Ghent)
2 & 3 September
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 ChimeraX. 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.
Up-front preparation:
- 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
Day 1:
Display protein structure data and compare structures, through the use of ChimeraX.
Create high-quality graphical representations of the structures.
Use FoldSeek to search for similar 3D structures
Various practical examples of studying effects of protein mutations
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
Dive in your research question where structural prediction via AlphaFold will be used
Use AlphaPulldown to execute protein-protein interaction screens using AlphaFold
A broader perspective on other protein folding predictors (ESMFold, OpenFold, RoseTTaFold) and AlphaFold3 as newest kid on the block.
You are encouraged to use your own laptop.
ChimeraX
MutateX
AlphaFold2
AlphaPulldown
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'.
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
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 (ChimeraX)
Comparing structures
FoldSeek - finding distantly related 3D structures
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
02 September 2024 - 03 September 2024
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
02 September 2024 - 03 September 2024
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
02 September 2024 - 03 September 2024
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.
02 September 2024 - 03 September 2024
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.
02 September 2024 - 03 September 2024
Ghent - VIB/UGent FSVM II
Course venue: L4