Introduction to Protein Structure Analysis

Introduction to Protein Structure Analysis

Target Audience:

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.

Objectives
  • 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.
Required skills

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).

Software demonstrated

Trainers

Alexander Botzki

Alexander Botzki is head of the VIB Bioinformatics Core

Contact Alexander Botzki :

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

iGent

Technologiepark-Zwijnaarde 126
9052 Gent
Belgium

18 February 2020

iGent
Public transport

Several buses drive between Gent Sint-Pieters railway station and Technologiepark: Bus 70, 71 and 72 (‘Tramstraat’)

  • Get off at the stop marked 'Bollebergen' at Grote Steenweg Noord.

  • Technologiepark is straight in front of you on the other side of the soft verge.

  • Walk into the park to the roundabout. You can see the iGent Tower on your left.

Shuttle bus

  • 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).

  • The site has four stops, including one nearly in front of the iGent Tower (4th stop).

  • More info on the Tech Lane Ghent Science Park site.

18 February 2020

iGent
Parking

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.

18 February 2020

iGent

Contact

VIB training
Tel: +32 9 244 66 11
Mail: training@vib.be