Lectures

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From sequence to 2D structure:

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


Ivo Hofacker (TBI Vienna, Austria)

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From sequence to 3D structure
Marcin Magnus (Harvard University)

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

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Modeling RNA-ion interactions
Elise  Duboué-Dijon (LBT, CNRS, Paris)

  • overview of the topic : why does it matter, why is it challenging, what do we know, what is still unclear?
  • basics in MD simulations, including advanced force field approaches (e.g. polarisable ff)
  • Various approach to capture ion-RNA interactions: explicitly polarizable force fields, implicit polarization approaches
  • how to assess the performance of these approaches?
  • the sampling problem: possible ways to solve it?

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Algorithms for RNA design
Sebastian Will (LIX, Ecole Polytechnique, France)

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

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Modeling RNA-protein interactions

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

Kalli Kappel (UCLA, Los Angeles, USA)

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Integrative RNA modeling

  1. SAXS and MD simulations: Liuba Mazzanti (BioCIS, Paris-Saclay Univ, France)
  • SAXS-driven molecular dynamics simulations for RNA folding
  • NMR constraints on RNA 3D structure molecular modeling
  • Cryo-EM maps for single structure modeling and ensemble refinements

Minimal requirements:

  • GROMACS
  • python (numpy, matplotlib)
  • ChimeraX

2. SHAPE probing: Ivo Hofacker (TBI Vienna, Austria)

  • Chemical probing methods
  • From reactivities to pseudo-energies
  • Structure ensembles
  • Mutate and map
  • Crosslinking methods

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RNA-based Therapeutics and Biotechnology

Michael Wolfinger

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