Protein Structure Analysis (Workshop as a Service)

Jun
15
June 15, 2018, 9:30 am
June 15, 2018, 5:00 pm
Where

VIB-UGent Research Building
PC room V114 (first floor)
Technologiepark 927
9052 Ghent
Belgium

 

This training is organised in the framework of the ELIXIR Implementation study “Using clouds and VMs for bioinformatics training”.

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 homologous structures. We will use online tools to quantify various interactions in the structures. ​The CSC Cloud service of ELIXIR Finland will be deployed.

Goals:

  • 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

Training schedule:

  • 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 modelling

 This event is organised by the VIB Bioinformatics Core and ELIXIR Belgium, and supported by ELIXIR Finland and the ELIXIR Hub Implementation Study.