Name: Joint Integrative Computational Biology workshop and CAPRI Meeting
Start: 2024-02-12T11:00:00+01:00
End: 2024-02-16T13:30:00+01:00
Location: EPN Campus

Monday, February 12, 2024

11:00 AM

11:00 AM - 1:30 PM
Room: IBS building / lobby

12:00 PM lunch
lunch
12:00 PM - 1:30 PM

1:30 PM

1:30 PM - 1:40 PM
Room: IBS seminar room
1:40 PM Chair: Sergei Grudinin
Chair: Sergei Grudinin
1:40 PM - 3:20 PM
Room: IBS seminar room
Contributions

1:40 PM Integrative modeling meets deep learning: applications to crosslinking mass spectrometry - Dina Schneidman (The Hebrew University of Jerusalem)

2:05 PM Analysis of protein-nucleic acid interactions in the PPI3D web server - Justas Dapkunas (Vilnius University)

2:30 PM Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling - Anila Sebastian (Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.)

2:55 PM VTX: High-performance molecular structure and dynamics visualization - Matthieu Montes (Conservatoire National des Arts et Métiers)
3:20 PM Coffee Break
Coffee Break
3:20 PM - 3:50 PM
Room: IBS building / lobby
3:50 PM Chair: Dina Schneidman
Chair: Dina Schneidman
3:50 PM - 5:55 PM
Room: IBS seminar room
Contributions

3:50 PM Generating backbone conformational changes with seven league boots - Frederic Cazals (Inria)

4:15 PM Analysis of interfaces in protein complexes using Voronoi tessellations and graph neural networks - Kliment Olechnovic (CNRS Laboratoire Jean Kuntzmann, Grenoble)

4:40 PM Complementarity based peptide docking and design - Alisa Khramushin (EPFL)

5:05 PM Protein structure evolution and convergence - Mathilde Carpentier (SU - MNH - CNRS)

5:30 PM Hybrid methods for analyzing conformational variability in cryo-EM and cryo-ET data - Slavica Jonic (CNRS & Sorbonne University, Paris)
5:55 PM

5:55 PM - 8:00 PM
Room: IBS building / lobby
Tuesday, February 13, 2024
8:10 AM Chair: Frédéric Cazals
Chair: Frédéric Cazals
8:10 AM - 9:50 AM
Room: IBS seminar room
Contributions

8:10 AM Generative models and analysis tools for the study of highly-flexible (intrinsically disordered) proteins - Juan Cortés (LAAS-CNRS)

8:35 AM Dissecting peripheral protein-membrane interfaces - Nathalie Reuter (University of Bergen)

9:00 AM Spectral partitioning into protein structural domains - Edoardo Sarti (Inria)

9:25 AM Integrative structure of a histone chaperone-histone complex - Hugo van Ingen (Utrecht University)
9:50 AM Coffee Break
Coffee Break
9:50 AM - 10:20 AM
Room: IBS building / lobby
10:20 AM Chair: Juan Cortès
Chair: Juan Cortès
10:20 AM - 12:00 PM
Room: IBS seminar room
Contributions

10:20 AM Exploring the conformational space of proteins by enumeration in the frame of the Distance Geometry Problem - Therese Malliavin (Laboratoire de Physique et Chimie Theoriques)

10:45 AM Integrative spatiotemporal map of nucleocytoplasmic transport - Barak Raveh (Hebrew University of Jerusalem)

11:10 AM Integrative modeling of protein oligomers using Heligeom - Chantal Prévost (CNRS et univ Paris Cité)

11:35 AM Asymmetric hydrophobic mismatch in assembly of ATP synthase rotor ring - Ivan Gushchin (Moscow Institute of Physics and Technology)
12:00 PM Lunch
Lunch
12:00 PM - 1:45 PM
1:45 PM Chair: Monste Soler-Lopez
Chair: Monste Soler-Lopez
1:45 PM - 3:25 PM
Room: IBS seminar room
Contributions

1:45 PM Integrative ensemble modeling that utilizes distance distribution restraints - Gunnar Jeschke (ETH Zürich)

2:10 PM Mechanistic study of MexAB-OprM efflux pump by an integrative approach - Isabelle Broutin (université Paris Cité)

2:35 PM Challenges in visualizing structural flexibility of the SAGA complex - Gabor Papai (INSERM)

3:00 PM Deciphering protein conformational dynamics with cryo-EM and MD simulations - Rémi Vuillemot (LJK, Université Grenoble Alpes, France)
3:25 PM Coffee break
Coffee break
3:25 PM - 3:55 PM
Room: IBS building / lobby
3:55 PM Chair: Matin Weik
Chair: Matin Weik
3:55 PM - 5:10 PM
Room: IBS seminar room
Contributions

3:55 PM Mariage of Cryo-EM, Solution Scattering, and Computational Science - Masaaki Sugiyama (Kyoto University, Institute for Integrated Radiation and Nuclear Science)

4:20 PM Protein Dynamics at extreme Temperatures - Beatrice CAVIGLIA (Universite' Paris Cite', University of Perugia)

4:45 PM POU5F1B and GOLPH3, two challenging proteins in structural biology - Maria Marcaida (EPFL)
5:10 PM Coffee break
Coffee break
5:10 PM - 5:40 PM
Room: IBS building / lobby
5:40 PM Chair: Gunnar Jeschke
Chair: Gunnar Jeschke
5:40 PM - 6:55 PM
Room: IBS seminar room
Contributions

5:40 PM Integrative structural biology of cell extracts : an application to structurally undercharacterized organisms - Ambroise Desfosses (CNRS- IBS)

6:05 PM Ensemble based calculations of spin-spin couplings in proteins: from ordered to disordered peptides - Amina Gaffour

6:30 PM Hinge disulfides in human IgG2 CD40 antibodies modulate receptor signaling by regulation of conformation and flexibility - Hayden FISHER (ESRF)
6:55 PM Free evening
Free evening
6:55 PM - 8:00 PM
Wednesday, February 14, 2024
8:30 AM Chair: Martin Blackledge
Chair: Martin Blackledge
8:30 AM - 9:45 AM
Room: IBS seminar room
Contributions

8:30 AM Intrinsically disordered regulators of endocytosis - an integrated NMR/single molecule fluorescence approach - Sigrid Milles (Forschungsverbund Berlin e.V. (FMP))

8:55 AM The Influence of Globular Domains on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation - Michael Bakker (Charles University)

9:20 AM Integrative Biology to tackle mitochondrial respiration in Alzheimer’s pathogenesis - Montserrat Soler Lopez (ESRF)
9:45 AM Coffee Break
Coffee Break
9:45 AM - 10:15 AM
Room: IBS building / lobby
10:15 AM Chair: Sigrid Milles
Chair: Sigrid Milles
10:15 AM - 11:30 AM
Room: IBS seminar room
Contributions

10:15 AM NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins involved in Viral Replication - martin blackledge

10:40 AM Structure and function relationships in protein homorepeats - Pau BERNADO (Centre de Biologie Structural (CBS-Montpellier))

11:05 AM Integrative structural biology with atomic force microscopy data - Jean-Luc Pellequer (IBS)
11:30 AM

11:30 AM - 12:30 PM
Room: IBS seminar room

12:30 PM Lunch
Lunch
12:30 PM - 2:00 PM

2:00 PM

2:00 PM - 2:15 PM
Room: IBS seminar room
2:15 PM
2:15 PM - 3:30 PM
Room: IBS seminar room
Contributions

2:15 PM CAPRI 2024: Pre- and post-Alphafold protein docking - Marc Lensink (CNRS)

3:00 PM Integrated pipeline for protein docking with extended and enhanced Alphafold-based modeling methods - Daisuke Kihara (Purdue University)
3:30 PM Coffee Break + posters
Coffee Break + posters
3:30 PM - 4:15 PM
Room: IBS building / lobby
4:15 PM
4:15 PM - 6:15 PM
Room: IBS seminar room
Contributions

4:15 PM Towards integrative use of pyDock and AI-based modeling in 8th CAPRI - Juan Fernandez-Recio (ICVV-CSIC and BSC)

4:45 PM Prediction and refinement of protein assemblies with ClusPro, Alphafold and Molecular Dynamics. - Dima Kozakov (Stony Brook University)

5:15 PM MassiveFold: optimized massive sampling with AlphaFold2 - Guillaume Brysbaert (CNRS University of Lille)

5:45 PM From Interaction Prediction to Sequence Design: Unveiling PeSTo's Potential in Structural Biology - Lucien Krapp (Laboratory for Biomolecular Modeling, EPFL)
Thursday, February 15, 2024
9:00 AM
9:00 AM - 10:30 AM
Room: IBS seminar room
Contributions

9:00 AM Impact of AI-Based Modeling on the Accuracy of Protein Assembly Prediction: The CASP Perspective - Ezgi Karaca (Izmir Biomedicine and Genome Center, DEU)

9:30 AM What have we learned (and memorized) about peptide-mediated interactions in CAPRI and beyond? - Ora Schueler-Furman (Hebrew University of Jerusalem)

10:00 AM HADDOCK in latest CAPRI rounds - Marco Giulini (Utrecht University) Victor Reys (Utrecht University)
10:30 AM Coffee Break + posters
Coffee Break + posters
10:30 AM - 11:00 AM
Room: IBS building / lobby
11:00 AM
11:00 AM - 12:15 PM
Room: IBS seminar room
Contributions

11:00 AM Assessing the impact of single-point mutations and alternative splicing-induced variations on protein-protein interactions - Elodie Laine

11:30 AM The Expanding Horizon of Protein Interactions - Shoshana Wodak (VIB-VUB Center doe Structural Biooogy, Brussels Belgium)
12:15 PM Lunch
Lunch
12:15 PM - 2:00 PM
2:00 PM
2:00 PM - 3:30 PM
Room: IBS seminar room
Contributions

2:00 PM Multistage Docking Approach for Protein-RNA Interactions Prediction in CAPRI and CASP - Shan Chang (Jiangsu University of Technology)

2:30 PM An Iteratively Derived Knowledge-based Scoring Function at Atomic Level for Protein-DNA Complexes Evaluations - XIaoqin Zou (University of Missouri - Columbia)

3:00 PM FTDMP: a framework for protein-protein, protein-DNA and protein-RNA docking and scoring - Rita Banciul (Vilnius University) Justas Dapkunas (Vilnius University)
3:30 PM Coffee Break + posters
Coffee Break + posters
3:30 PM - 4:15 PM
Room: IBS building / lobby
4:15 PM
4:15 PM - 5:30 PM
Room: IBS seminar room
Contributions

4:15 PM Interpretable Affinity Prediction and Generative Design for Protein-Ligand Interactions - Yang Shen (Texas A&M University)

4:45 PM Automated protein-to-Structure pipelines for new structures and X-ray based ligand screening at EMBL Grenoble. Experience from our first collaboration with CAPRI - José Márquez (EMBL Grenoble)
5:30 PM

5:30 PM - 6:30 PM
Room: IBS seminar room

7:30 PM

7:30 PM - 10:30 PM
Friday, February 16, 2024
9:00 AM
9:00 AM - 10:00 AM
Room: IBS seminar room
Contributions

9:00 AM Shape retrieval methods for the classification of protein surfaces - Grisell Diaz Leines (EMBL-EBI)

9:30 AM High-throughput prediction of ATP synthase rotor ring stoichiometries - Ivan Gushchin (Moscow Institute of Physics and Technology)
10:00 AM Coffee Break + posters
Coffee Break + posters
10:00 AM - 10:30 AM
Room: IBS building / lobby
10:30 AM
10:30 AM - 11:30 AM
Room: IBS seminar room
Contributions

10:30 AM Unsupervised Machine Learning and Phase Space Reduction: A Robust and Generalisable Approach for Concurrently Solving the Protein Complex Conformation Classification and Quantification Problems. - Daniel Celis Garza (CCP4, Research Complex at Harwell, STFC Rutherford-Appleton Laboratory, UK)

11:00 AM Modeling of immune recognition and protein complexes with deep learning and physics-based docking - Brian Pierce (University of Maryland)
11:30 AM Closure
Closure
11:30 AM - 12:00 PM
Room: IBS seminar room

12:00 PM Lunch at the canteen
Lunch at the canteen
12:00 PM - 1:30 PM