**Goal: **To hold focused meetings on hot topics in structural bioinformatics

**When: **5-8 December 2022

**Where: **Paris Sorbonne Université, Jussieu

**Organizers:** Frédéric Cazals (Sampling; Inria Sophia-Antipolis), Sergei Grudinin (ML), Yann Ponty, Alessandra Carbone

## Location

The events will be hosted by the Jussieu campus of Sorbonne Université in Paris, France.

Lectures will be delivered in the **C404** room located on the Jussieu campus (Metro Jussieu). Coffee breaks will be served in the **colibri** room.

## Program

Monday Dec 5th | ||

14:00-14:05 | Introduction – Welcome address | |

Machine Learning 1 | ||

14:05-14:35 | Vincent Mallet | Institut Pasteur |

Representations learning on the structure of biomolecules (abstract) | ||

14:35-15:05 | Yasser Mohseni Behbahani | Sorbonne Université |

Deep Local Analysis estimates effects of mutations on protein-protein interactions (abstract) | ||

15:05-15:35 | Dmitrii Zhemchuzhnikov | Université Grenoble Alpes |

6DCNN with Roto-Translational Convolution Filters for Volumetric Data Processing (abstract) | ||

15:35-16:20 | Coffee break | |

16:20-16:50 | Valentin Lombard | LCQB |

Toward a comprehensive description of protein conformational diversity (abstract) | ||

16:50-17:20 | Pablo Chacon | Institute of Physical Chemistry (IQFR-CSIC) |

Geometric Algebra Models of Proteins for learning orientations (abstract) | ||

17:20-18:00 | Free discussions | |

Tuesday Dec 6th | ||

Machine Learning 2 | ||

9:00-9:50 | Martin Weigt | LCQB |

Generative models of biomolecular sequences (abstract) | ||

9:50-10:20 | Nicolas Buton | Data and Knowledge Management, Univ. Rennes, Inria, IRISA, Rennes, 35000, France |

Predicting enzymatic function of protein sequences with attention (abstract) | ||

11:00-11:20 | Yulia Kacher | Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France |

Proteins conformational space investigation: a machine learning approach to uncover missing intermediates (abstract) | ||

10:20-11:00 | Coffee break | |

11:20-11:40 | Romain Menegaux | INRIA |

Encoding graph structure in transformers (abstract) | ||

12:00-14:00 | Lunch break | |

14:00-14:20 | Stéphane Téletchéa | Nantes Université, US2B, CNRS, UMR6286, F-44000 Nantes |

Forces et faiblesses des méthodes de prédiction des structures de protéines (abstract) | ||

14:20-14:40 | Helene Bret | CEA / I2BC |

Modeling disordered regions in interactomes using AlphaFold (abstract) | ||

14:40-15:00 | Vaitea Opuu | Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany |

CARNAGE: structure-in-sequence compression with graph neural network (abstract) | ||

15:00-15:30 | Marianne Defresne | INSA Toulouse |

Protein Design with Automated Reasoning and Deep Learning (abstract) | ||

15:30-16:00 | Sergei Grudinin | LJK CNRS |

News from CASP15 and Discussion topics (abstract) | ||

16:00-18:00 | Coffee break and Discussion | |

Wednesday Dec 7th | ||

Sampling 1 | ||

8:45-9:40 | Jérôme Hénin | CNRS – IBPC |

Tools for exploring molecular free energy landscapes using mostly natural (and some artificial) neural networks (abstract) | ||

9:40-10:35 | Gabriel Stoltz | Ecole des Ponts |

Coarse-graining and efficiently sampling with autoencoders (abstract) | ||

10:30-11:00 | Coffee break | |

11:00-12:00 | Elias Tsigaridas | Inria Paris and IMJ-PRG |

Geometric random walks and sampling from convex bodies (abstract) | ||

12:00-14:00 | Lunch break | |

14:00-14:45 | Augustin Chevallier | Université Strasbourg |

Sampling using Piecewise Deterministic Markov Processes (abstract) | ||

14:45-15:50 | David Wales | University of Cambridge |

Energy landscapes: from machine learning to enhanced sampling (abstract) | ||

15:50-16:20 | Coffee break | |

16:20-17:00 | Samuela Pasquali | Université Paris Cité |

Modeling RNA Polymorphism (abstract) | ||

Thursday Dec 8th | ||

Sampling 2 | ||

8:45-9:40 | Tony Lelievre | Ecole des Ponts |

Sampling probability measures on submanifolds (abstract) | ||

9:40-10:35 | Juan Cortés | CNRS |

A unified computational method with reinforcement learning for modeling conformational ensembles of complex protein architectures (abstract) | ||

10:35-11:05 | Coffee break | |

11:05-12:00 | Frederic Cazals | Inria |

Sampling molecular conformations with seven-league boots: can we reconcile structure and thermodynamics? (abstract) | ||

12:00-14:00 | Lunch break |

## Abstracts

## Participants

Elena Álvarez Sánchez | Nantes Université, US2B, CNRS, UMR6286, F-44000 Nantes, France / Affilogic, SAS, Nantes, France |

Marina Abakarova | LCQB |

Samia Aci-Sèche | CNRS |

Camille Alliot | Université de paris cite |

Diego AMAYA | INRIA Nancy Grand Est |

Jessica Andreani | CEA I2BC |

Benjamin Bardiaux | CNRS-Institut Pasteur |

Clément Bernard | Laboratoire IBISC |

Vadim BERTRAND | UGA |

WARDA BOUTEGRABET | Institut Mondor de recherche biomédicale |

Costas Bouyioukos | Université Paris Cité |

Helene Bret | CEA / I2BC |

Nicolas Buton | Data and Knowledge Management, Univ. Rennes, Inria, IRISA, Rennes, 35000, France |

Alessandra Carbone | Sorbonne Université – LCQB |

Mathilde Carpentier | Sorbonne Université |

Frederic Cazals | Inria |

Maud CHAN YAO CHONG | QST institute |

Augustin Chevallier | Université Strasbourg |

Nathalie Colloc’h | ISTCT UMR 6030 CNRS Université de Caen-Normandie |

Juan Cortés | CNRS |

François Coste | Inria |

Wagner Alan Aparecido DA ROCHA | Laboratoire d’informatique de l’École polytechnique |

Davy DARANKOUM | Laboratoire Jean Kuntzmann |

Rajkumar Darbar | xxx |

Isaure de Beauchêne | CNRS |

Sjoerd de Vries | CNRS |

Élise Duboué-Dijon | Laboratoire de biochimie théorique |

Elodie Duprat | Sorbonne Université (IMPMC) |

Delphine Flatters | Université Paris Cité |

Tatiana Galochkina | DSIMB, UMRS 1134 – Inserm et Université Paris Cité |

Aria Gheeraert | INSERM |

Paraskevi Gkeka | Sanofi R&D |

Nohad Gresh | LCT UMR 7616 CNRS |

Sergei Grudinin | LJK CNRS |

Konrad Hinsen | CNRS – Centre de Biophysique Moléculaire |

Samuel Holvec | Institut de Génétique et de Biologie Moléculaire et Cellulaire – illkirch |

Jérôme Hénin | CNRS – IBPC |

Diego Inostroza | Laboratoire de Chimie Théorique |

Laurent Jacob | CNRS |

Slavica JONIC | CNRS & Sorbonne Université |

Yulia Kacher | Universite de Lorraine |

Yasaman Karami | Institut Pasteur |

Florencia Klein | Laboratoire de Biochimie Théorique-Institut de Biologie Physico-Chimique (IBPC) |

Anna Kravchenko | LORIA |

Louis Lagardère | Sorbonne Université |

Elodie Laine | Sorbonne Université |

Olivier Languin-Cattoën | Laboratoire de Biochimie Théorique – IBPC |

Benoist LAURENT | CNRS |

Quoc Khang Le | Paris-Saclay Unversity |

Fabrice Leclerc | I2BC CNRS-CEA-Univ. Paris Saclay |

Julie Ledoux | ENS Paris-Saclay |

Tony LELIEVRE | Ecole des Ponts |

Valentin Lombard | LCQB |

Gianluca Lombardi | Laboratoire LCQB, Sorbonne Université |

Irene Maffucci | Université de technologie de Compiègne – UMR 7025 |

Ikram Mahmoudi | Doctorante |

Bernard Maigretr | LORIA – CNRS, INRIA, Université de Lorraine |

Vincent MALLET | Institut Pasteur |

Therese Malliavin | Laboratoire de Physique et Chimie Theorique, Université de Lorraine et CNRS |

R. Charbel Maroun | INSERM U1204 |

R. Charbel Maroun | UMR-S U1204 INSERM/U-Paris Saclay |

Juliette Martin | CNRS |

Romain Menegaux | INRIA |

Dominique MIAS | LORiA |

David Mignon | Laboratoire BIOC, Ecole Polytechnique |

Yasser MOHSENI BEHBAHANI | Sorbonne Université |

Samuel Murail | Université Paris Cité |

Roberto Netti | LCQB |

Phuong NGUYEN | Laboratoire de Biochimie Théorique, UPR9080 CNRS, 13 rue Pierre et Marie Curie, 75005 Paris |

Khanh-Chi NGUYEN-PHAM | Université Grenoble Alpes |

Khanh-Chi NGUYEN-PHAM | University Grenoble Alpes |

Maxence Noble | Ecole Polytechnique |

Loïc Omnes | Laboratoire IBISC – université d’Evry |

vaitea opuu | Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany |

Nicolas Panel | Toulouse Biotechnology Institute |

Marco Pasi | ENS Paris-Saclay |

samuela pasquali | Université Paris Cité |

Thomas Pigeon | INRIA – IFPEN |

Jean-Philip PIQUEMAL | Sorbonne Université |

Lélia Polit | LCQB |

Yann Ponty | CNRS/Ecole Polytechnique |

Chantal Prévost | Laboratoire de Biochimie Théorique – IBPC – CNRS |

Ivan Reveguk | Ph.D. student, BIOC, Ecole Polytechnique, Palaiseau |

Ivan Reveguk | PhD Student in BIOC, Ecole Polytechnique |

Charles ROBERT | CNRS Laboratorie de Biochimie Théorique, IBPC Paris 5ème |

Klypa Roman | Ecole Polytechnique |

Gaspar Roy | Institut de Recherche pour le Développement |

Seyedehafra Sabei | Laboratoire de Biochimie Théorique – IBPC – CNRS (future doctorante) |

Edoardo Sarti | Inria |

Vittore Scolari | Institut Curie |

Thomas Simonson | CNRS/Ecole Polytechnique |

Gabriel Stoltz | Ecole des Ponts |

Dirk Stratmann | Sorbonne Université |

Fariza TAHI | IBISC. Univ Evry, Université Paris-Saclay |

Antoine Taly | CNRS-Laboratoire de Biochimie Théorique |

Antoine Taly | CNRS- Laboratoire de Biochimie Théorique |

Mounir Tarek | CNRS- Université de Lorraine |