EMBO Practicuum: Computational Analysis of PPIs for Bench Biologists

"" " As a result of attending the course, trainees should be better able to:

  • Identify previously-reported data on PPIs from databases
  • Use bioinformatics tools to predict protein modules from protein sequences
  • Visualise and analyse data on the 3D structure of PPIs, and of PPI networks
  • Describe ways in which PPIs have been targeted, using bioinformatics approaches, in drug design
  • Describe the characteristics of PPIs mediated between different kinds of protein modules


Tools used and practical exercises taught will focus on the following use-cases:

  1. retrieving previously-reported PPI data associated with protein(s) of interest (and other kinds of data), using resources such as UniProt, IntAct, MINT, ePDB/PDB, PhosphoELM, REFLECT, and others
  2. predicting protein interaction modules from protein sequence, using resources such as PFAM, SMART, InterPro, ELM, IUPRED, ScanSite, and others
  3. identifying modules in PPI networks, and predicting their function, using resources such as STRING, STITCH, and Cytoscape
  4. identifying residues likely to be involved in direct physical contact between proteins in PPIs, using resources such as CLUSTALX, JalView, PyMOL, and PISA


Additionally, practicals will focus on developing the participants' understanding of several key concepts including: interpretation of sequence alignments; concepts associated with protein 3D structure; the structural diversity of PPIs; and structures of biological databases.
In several cases, developers of the packages used during the course are trainers in the course (Toby Gibson, ELM, CLUSTALX; Zsuzsanna Dosztanyi, IUPRED; Michael Yaffe; ScanSite; Francesca Diella: PhosphoELM, ELM; Lars Juhl Jensen: STRING, STITCH, REFLECT; Gary Bader and Piet Molenaar, Cytoscape).  " ""




"Nanotechnology for the biologist"

Journal of Leukocyte Biology vol. 78 no. 3 585-594

September 2005



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