Lectures

Important: Please do install at your earliest convenience all necessary tools/dependencies before hands-on sessions.

Introductory lectures

By Antoine Taly (CNRS/IBPC, Univ. Paris Cité)

  1. Monday – RNA data, structure representations and black boxes [Slides]
  2. Tuesday – RNA partners, allostery and the dimensionality of models [Slides]
  3. Thursday – Our responsibility and the importance of documenting modeling choices [Slides]
  4. Friday – RNA design and the cost of drugs [Slides]

From sequence to 2D structure

Lecture by Ivo Hofacker (TBI, Univ. Vienna, Austria)
Assisted by Leonhard Sidl (TBI, Univ. Vienna, Austria)
[Lecture slides 1] [Lecture slides 2]
[Hands on instructions]
[Hands on assignment] [Hands on slides]

  1. Basics of RNA 2D and 3D structure
  2. The nearest neighbor energy models
  3. RNA folding by Dynamic Programming
  4. Minimum free energy structures
  5. Partition-function and pair probabilities
  6. Suboptimal structure prediction
  7. MEA and centroid structures
  8. Extensions to Pseudoknots, G-quadruplexes
  9. RNA-RNA interactions

Modeling RNA-protein interactions

Lecture by Kalli Kappel (UCLA, Los Angeles, USA)
[Lecture slides]
[Hands on instructions]
[Detailed instructions to install Draffter]

  1. Intro to 3D structures of RNA-protein complexes and general principles
  2. Overview of experimental techniques
  3. Overview of existing experimental data
  4. Physics- and knowledge-based computational approaches to modeling RNA-protein complexes
  5. Deep learning methods for modeling RNA-protein complexes

From sequence to 3D structure

Lecture by Marcin Magnus (Harvard University)
[Lecture slides]
[Hands on instructions]

  1. RNA 3D structure: why secondary structure isn’t enough — and when structure actually matters
  2. RNA 3D structure prediction with AlphaFold3
  3. RNA–protein interfaces modeling with Flow Matching models
  4. (maybe) Sequence Is All You Need! – sequence design (including therapeutics) with Large Language Models

Modeling RNA-ion interactions

Lecture by Elise Duboué-Dijon (LBT, CNRS, Paris)
[Lecture slides]

  1. Topic overview: why does it matter, why is it challenging, what do we know, and what is still unclear?
  2. MD simulations basics, including advanced force field approaches (e.g. polarisable ff)
  3. Various approach to capture ion-RNA interactions: explicitly polarizable force fields, implicit polarization approaches
  4. How to assess performances of these approaches?
  5. The sampling problem: possible ways to solve it?

Algorithms for RNA design

Lecture by Sebastian Will (LIX, Ecole Polytechnique, France)
Assisted by Hua-Ting Yao (TBI, Univ. Vienna, Austria)
[Lecture slides]
[Hands on instructions]

  1. Intro to RNA design: Positive and negative design objectives
  2. Complex positive design powered by tree-decomposition and declarative modeling
  3. Negative design by stochastic optimization
  4. Brief intro to generative models for design

Integrative RNA modeling 1: SAXS and MD simulations

Lecture by Liuba Mazzanti (BioCIS, Paris-Saclay Univ, France)
[Lecture slides]
[Hands on instructions]

  1. SAXS-driven molecular dynamics simulations for RNA folding
  2. NMR constraints on RNA 3D structure molecular modeling
  3. Cryo-EM maps for single structure modeling and ensemble refinements

Integrative RNA modeling 2: SHAPE probing

Lecture by Ivo Hofacker (TBI Vienna, Austria)
[Lecture slides]
[Practicals for hands on session]

  1. Chemical probing methods
  2. From reactivities to pseudo-energies
  3. Structure ensembles
  4. Mutate and map
  5. Crosslinking methods

RNA-based Therapeutics and Biotechnology

Lecture by Michael T Wolfinger (TBI/RNA Forecast)
[Lecture slides]

  1. Introduction to RNA-based approaches in modern medicine
  2. Overview of nucleoside analogues as antiviral agents, diving a bit into lethal mutagenesis & error catastrophe concepts
  3. Conceptual basis of RNA aptamers and their application, possibly with some of our current research mixed in
  4. Molecular principles underlying RNA as target and as drug
  5. Outlook on future directions in RNA therapeutics