Lectures are from 9 AM to noon, Practicals from 2 to 5 PM.

Links to lecture notes and practicals info will be added to each day as needed.

Monday, 23 Nov: Peter Tompa

Peter Tompa, Vrije Universiteit Brussels, Belgium

Introduction and overview of IDPs: from theory to practice

Image of p53 protein bound to DNA

A general introduction to intrinsically disordered proteins through a historical perspective to the most recent developments.

In the theory part, we will cover:

  • brief history and basic concepts
  • biophysical methods for the characterization of structural disorder
  • functions and functional classification of disordered proteins
  • structural disorder in diseases: can we target IDPs?

In the practical part, we will look into data and bioinformatics approaches to structural disorder, such as:

  • databases of disordered proteins: DisProt, MobiDB, PED and PhaSePro
  • bioinformatics tools: prediction of structural disorder and comparison of disordered ensembles
  • low-complexity sequences, prion-like domains and bioinformatics of phase-separating proteins

Monday, 23 Nov, after the practical: Participants Session

Short presentations (≤5 min) to tell about your research interests

Please have a couple of slides (pdf format) ready to project.

Tuesday, 24 Nov: Gerhard Hummer

Gerhard Hummer, Max Planck Institute for Biophysics, Frankfurt am Main, Germany

Sampling the conformational space, structural, thermodynamic and kinetic modelling

[Pietrek, Stelzl, & Hummer, J. Chem. Theory Comput. 2020]

Description of morning lecture and afternoon practical session coming soon!

Wednesday, 25 Nov: Martin Blackledge and Nathalie Sibille

Martin Blackledge, Institut de Biologie Structurale, Grenoble, France

Nathalie Sibille, Centre de Biochimie Structurale de Montpellier, France

Connecting conformational ensembles to experimental results

Description of morning lecture and afternoon practical session coming soon!

Thursday, 26 Nov: Jeetain Mittal

Jeetain Mittal, Dept Chemical and Biomolecular Engineering, Lehigh Univ, Pennsylvania

Phase Separation in the Cell

The morning lecture and the afternoon practical will cover physics-based computational models that we have been developing in close collaboration with experimental collaborators for the last ten years.

The lecture will provide a broad overview of available atomistic and coarse-grained models and their relative benefits for specific research problems. A particular emphasis will be a discussion of models suitable for studying the liquid-liquid phase separation of proteins and nucleic acids.

The practical will cover the software and scripts necessary to use our coarse-grained modeling framework capable of providing molecular-level details on the sequence-determinants of protein phase separation due to specific disease mutations and the inclusion of a folded domain, and variation of chain length.

Friday, 27 Nov: Juan Cortés and Frédéric Cazals

Juan Cortés, CNRS LAAS, Toulouse, France

Frédéric Cazals, Inria, Sophia-Antipolis

Novel algorithms for exploring and characterizing high-dimensional conformational spaces

Robot path-planning for IDP conformations Simplifying a complex PEL

Part I:

  • Modeling proteins in internal coordinates: a robotics-inspired approach
  • Tripeptides as basic elements to model highly-flexible proteins and regions
  • Structural propensity prediction from IDP sequences based on a structural database of tripeptides
  • Generation of conformational ensemble models of IDPs/IDRs

Part II:

  • Distance based structural measures: least RMSD and combined RMSD
  • Nearest neighbor graphs of conformations and energy landscape models
  • Persistence based analysis of energy landscapes
  • Applications to IDPs


  1. Predicting secondary structure propensities in IDPs using simple statistics from three-residue fragments; A. Estaña, A. Barozet, A. Mouhand, M. Vaisset, C. Zanon, P. Fauret, N. Sibille, P. Bernadó, J. Cortés; Submitted.
  2. Realistic ensemble models of intrinsically disordered proteins using a structure-encoding coil database; A. Estaña, N. Sibille, E. Delaforge, M. Vaisset, J. Cortés, P. Bernadó; Structure, 27(5): 381-391.e2, 2019
  3. A reinforcement-learning-based approach to enhance exhaustive protein loop sampling; A. Barozet, K. Molloy, M. Vaisset, T. Siméon, J. Cortés; Bioinformatics, 36(4): 1099-1106, 2020
  4. Characterizing molecular flexibility by combining lRMSD measures; F. Cazals, and R. Tetley; Proteins, 87 (5), 2019.
  5. Energy landscapes and persistent minima; J. Carr, and D. Mazauric, and F. Cazals, and D. Wales; The Journal of Chemical Physics, 144 (5), 2016
  6. Conformational Ensembles and Sampled Energy Landscapes: Analysis and Comparison; F. Cazals, and T. Dreyfus, and D. Mazauric, and A. Roth, and C.H. Robert; J. Comp. Chem., 36 (16), 2015.

Friday afternoon: Bus back to the Ajaccio airport following the practical session.