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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Tags: EMBO, PPI, actomyosin, bioinformatics, biomolecular_nanostructures, cell_regulation, computational_analysis, computational_toxicology, datasets, linear_motif_biology, More…molecular_medicine, nano-acuators, nanomolar-affinity, post-translational_modification, predictive_science, protein-protein_interaction, protein_architecture, wet-lab


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Publications by A. Paszternák:

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Pd/Ni Synergestic Activity for Hydrogen Oxidation Reaction in Alkaline Conditions

The potential use of cellophane test strips for the quick determination of food colours

pH and CO2 Sensing by Curcumin-Coloured Cellophane Test Strip

Polymeric Honeycombs Decorated by Nickel Nanoparticles

Directed Deposition of Nickel Nanoparticles Using Self-Assembled Organic Template,

Organometallic deposition of ultrasmooth nanoscale Ni film,

Zigzag-shaped nickel nanowires via organometallic template-free route

Surface analytical characterization of passive iron surface modified by alkyl-phosphonic acid layers

Atomic Force Microscopy Studies of Alkyl-Phosphonate SAMs on Mica

Amorphous iron formation due to low energy heavy ion implantation in evaporated 57Fe thin films

Surface modification of passive iron by alkylphosphonic acid layers

Formation and structure of alkylphosphonic acid layers on passive iron

Structure of the nonionic surfactant triethoxy monooctylether C8E3 adsorbed at the free water surface, as seen from surface tension measurements and Monte Carlo simulations

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