Introduction to Protein Structure Analysis
General context
This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure. Different hands-on exercises will allow you to compare the structure of homologues, to predict a structural model of proteins (without any structure information) and to find homologuous structures. We will use online tools to quantify various interactions in the structures.
- 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 Yasara.
- Create high-quality graphical representations of the structures.
- Calculate the effect of mutations on the stability of your protein.
You are encouraged to use your own laptop. For those who do not have a laptop, the YASARA software can be run in a remote Linux environment (access to cloud via webbrowser).
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'.
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 (YASARA)
Comparing structures
Predicting the effect of point mutations on protein structures
Predicting protein structures of close homologues by homology modeling
Practical info
18 February 2020
Ghent - iGent
Technologiepark-Zwijnaarde 126
9052 Gent
Belgium
18 February 2020
Ghent - iGent
Several buses drive between Gent Sint-Pieters railway station and Technologiepark: Bus 70, 71 and 72 (‘Tramstraat’)
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Get off at the stop marked 'Bollebergen' at Grote Steenweg Noord.
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Technologiepark is straight in front of you on the other side of the soft verge.
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Walk into the park to the roundabout. You can see the iGent Tower on your left.
Shuttle bus
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The shuttle service between Gent Sint-Pieters and Technologiepark runs every 15 minutes during peak hours (7.30 - 9.30 am and 4.30 - 6.30 pm).
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The site has four stops, including one nearly in front of the iGent Tower (4th stop).
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More info on the Tech Lane Ghent Science Park site.
18 February 2020
Ghent - iGent
You can park your car on the Tech Lane Ghent Science park in the open car parks (no barriers), like the one in front of the iGent tower across the road. These car parks have Dutch signs which read "Parkeren uitsluitend met vignet! (overtreding = wielklem)”. This means you should only park there if you have a valid car park permit. You can request such a permit by sending an email to your contact person at iGent. The permit is only valid for a single day, and will need to be placed visibly behind the car's windscreen.