About
Understanding physical and functional interactions between molecules in living systems is crucial in many biological processes. Several powerful methods and techniques have been developed to generate molecular interaction data, focusing mainly on protein-protein interactions (PPIs). In particular, PPIs involving partially or completely unstructured regions are building blocks of regulatory and signalling networks that control cell response to external and internal cues. Exploring these interactions may help understanding a protein’s function and behavior, predicting biological processes that a protein of unknown function is involved in, and characterising protein complexes that can be used to modulate or perturb known biological processes and pathways.
The course is intended for PhD students and postdocs working in experimental biology, but scientist of all levels are welcome. Participants will be introduced to a wide variety of popular bioinformatic tools aimed at exploring and predicting PPIs. At the end of the course, participants should have an increased ability to:
- Find and use information on PPIs from diverse databases.
- Visualise and inspect 3D structure of PPIs and PPI networks.
- Predict protein modules such as globular domains, unstructured regions and short linear motifs (LMs), from the protein sequence.
- Portray the characteristics of PPIs between different types of protein modules.
- Become acquainted with current strategies to target PPIs for drug design.
- Biological database searches for information on PPI data associated to any protein of interest: UniProt, MINT, ePDB/PDB, among others.
- Exploration of PPI networks: STRING, STITCH, Cytoscape.
- Identification of residues responsible for the physical contact between proteins in PPIs using CLUSTALX, JalView, PyMOL, PISA.
- Prediction of protein interaction modules from protein sequence: using resources such as ELM, IUPRED, Anchor.
Application deadline
15 January 2017
Selected participants will be notified by
Early February
Speakers
- Alexandre Bonvin from Utrecht University, Utrecht
- Alessandra Carbone from Université Pierre et Marie Curie, Paris
- Freddy Cliquet from Institut Pasteur, Paris
- Javier de las Rivas from Cancer Research Center, Salamanca
- Zsuzsanna Dosztányi from Lorand Eotvos University, Budapest
- Toby Gibson from EMBL, Heidelberg
- Raphaël Guerois from Commissariat à l’énergie atomique et aux énergies alternatives, Paris
- Daniel Ladant from Institut Pasteur, Paris
- Sonia Longhi from AFMB, Marseille
- Olivier Sperandio from Institut Pasteur, Paris
- Pierre Tufféry from INSERM / Paris 7, Paris
- Benjamin Bardiaux from Institut Pasteur, Paris
- Claudia Chica from Institut Pasteur, Paris
- Natalia Pietrosemoli from Institut Pasteur, Paris
- Thomas Rolland from Institut Pasteur, Paris
Programme
Download the final schedule- 09:00 – 10:00 Registration.
- 10:00 – 11:15 Overview of experimental techniques to map PPI (Daniel Ladant)
- 11:15 – 11:45 Coffee break
- 11:45 – 13:00 PPI dedicated databases (Javier de las Rivas)
- 13:00 – 14:00 Self organized lunch
- 14:00 – 15:30 Hands on: Databases and tools for PPI visualization and analysis (Javier de las Rivas, Freddy Cliquet)
- 15:30 – 16:00 Coffee break
- 16:00 – 17:30 Hands on: Databases and tools for PPI visualization and analysis (Javier de las Rivas, Freddy Cliquet)
- 17:30 – 18:30 Welcome get together – Poster session
- 09:00 – 10:15 Structural modelling of protein-protein interactions using evolution (Raphaël Guerois)
- 10:15 – 10:45 Coffee break
- 10:45 – 12:00 Large-scale cross-docking to unravel protein-protein interactions: explored directions and progress (Alessandra Carbone)
- 12:00 – 14:00 Self organized lunch
- 14:00 – 15:30 Information-driven modelling of biomolecular interactions (Alexandre Bonvin)
- 15:30 – 16:00 Coffee break
- 16:00 – 17:30 Hands on: Protein-protein docking with HADDOCK (Alexandre Bonvin)
- 17:30 – 18:00 Flash talks from participants
- 09:00 – 10:15 Diversity of PPIs, modular protein architecture and the nature of cell regulation (Toby Gibson)
- 10:15 – 10:45 Coffee break
- 10:45 – 12:00 Protein disorder prediction and dedicated databases (Zsuzsanna Dosztányi)
- Free afternoon
- 09:00 – 10:30 Hands on: Linear motifs (LMs) resources and methods for LMs prediction (Toby Gibson)
- 10:30 – 11:00 Coffee break
- 11:00 – 12:30 Hands on: LMs resources and methods for LMs prediction (Toby Gibson)
- 12:30 – 14:00 Self organized lunch
- 14:00 – 15:30 Hands on: IUPRED, ANCHOR, DisProt, D2P2 (Zsuzsanna Dosztányi)
- 15:30 – 16:00 Coffee break
- 16:00 – 17:30 Hands on: IUPRED, ANCHOR, DisProt, D2P2 (Zsuzsanna Dosztányi)
- 17:30 – 18:00 Flash talks from participants
- 09:00 – 10:15 Considering protein interactions with smaller proteins: Protein-peptide interactions (Pierre Tufféry)
- 10:15 – 10:45 Coffee break
- 10:45 – 12:00 In silico drug design on protein-protein interactions (Olivier Sperandio)
- 12:00 – 14:00 Self organized lunch
- 14:00 – 15:30 A journey into structural disorder and induced folding in paramyxoviruses: an experimental perspective (Sonia Longhi)
- 15:30 – 16:00 Coffee break
- 16:00 – 17:00 Concluding remarks / Round table
- 17:00 – Social event
Course Material
Click the following link to access Course Material (restricted access)
Registration
Registration is compulsory yet free of charge. During the registration process you’ll need to specify whether you want to take the full course, i.e. assist to both theoretical and practical sessions, or just participate in the theoretical sessions. Selected participants of the full course are encouraged to present a poster or a 5 minutes talk (flash talk) on their research subject.
Registrations are close now
