ABOUT THE PRACTICAL COURSE

Protein-protein interaction data is being generated at an ever-increasing rate. Many scientists are not trained in the bioinformatics tools needed to analyse this data. Given the importance of this data in many life science disciplines, there is a major need to provide training in such tools; particularly for bench biologists (especially for researchers into pathogens such as HIV or tuberculosis, which reply on PPIs for their pathogenicity) who need to use, or generate themselves such data, but who do not have the theoretical background needed to assess it critically.

The diversity and importance of PPIs involving intrinsically disordered protein (IDP) regions has recently become clear, leading to considerable growth in bioinformatics tools for working with IDP data. Thus, another important component of our teaching will involve lectures on the theory and practical implications of these developments in our understanding of protein-protein interactions.

The EMBO Practical Course is aimed at bench scientists who are working with proteins, with a focus on identifying, predicting and analysing features of their interactions with other proteins. No prior knowledge of specific bioinformatics tools will be assumed. As part of the course, we will hold a bioinformatics unseminar (similar to these http://hub-hub.de and http://thecubhub.wordpress.com/) to have a chance for trainees to meet and network with other local bioinformaticans.

Topics taught during the course will include:

  • general principles of bioinformatics and protein modules
  • web resources describing results of PPI experiments
  • 3D protein structure perspective on PPIs
  • predicting protein modules from sequence (domains, motifs, IDP modules)
  • exploring PPI networks using STRING and Cytoscape
Tools taught during the course will include:
  • PFAM (predicting protein families from sequence)
  • SMART (predicting protein families from sequence)
  • STRING (visualisation, description, and prediction of PPI networks)
  • STITCH (integration of small molecules in PPI networks)
  • Cytsoscape (visualisation of networks)
  • CLUSTALX (visualisation and building of multiple sequence alignments)
  • JalView (visualisation and manipulation of multiple sequence alignments)
  • UniProt (data resource describing features of protein sequences)
  • Chimera (3D visualisation and analysis of biomolecular structures)
  • IUPred (prediction of intrinsically unstructured protein regions)
  • ELM (data resource and predictor of short protein linear motifs)
  • PhosphoELM (data resource and predictor of phosphorylated amino acids in proteins)

 

VENUE

 

   

Faculty of Health Sciences,

Barnard Fuller Building,
Anzio Road, 7925,

South Africa

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