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

Joint Integrative Computational Biology workshop and CAPRI Meeting

from Monday, 12 February 2024 (11:00) to Friday, 16 February 2024 (13:30)

Monday, 12 February 2024

11:00

11:00 - 13:30
Room: IBS building / lobby

12:00 lunch
lunch
12:00 - 13:30

13:30

13:30 - 13:40
Room: IBS seminar room
13:40 Chair: Sergei Grudinin
Chair: Sergei Grudinin
13:40 - 15:20
Room: IBS seminar room
Contributions

13:40 Integrative modeling meets deep learning: applications to crosslinking mass spectrometry - Dina Schneidman (The Hebrew University of Jerusalem)

14:05 Analysis of protein-nucleic acid interactions in the PPI3D web server - Justas Dapkunas (Vilnius University)

14:30 Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling - Anila Sebastian (Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.)

14:55 VTX: High-performance molecular structure and dynamics visualization - Matthieu Montes (Conservatoire National des Arts et Métiers)
15:20 Coffee Break
Coffee Break
15:20 - 15:50
Room: IBS building / lobby
15:50 Chair: Dina Schneidman
Chair: Dina Schneidman
15:50 - 17:55
Room: IBS seminar room
Contributions

15:50 Generating backbone conformational changes with seven league boots - Frederic Cazals (Inria)

16:15 Analysis of interfaces in protein complexes using Voronoi tessellations and graph neural networks - Kliment Olechnovic (CNRS Laboratoire Jean Kuntzmann, Grenoble)

16:40 Complementarity based peptide docking and design - Alisa Khramushin (EPFL)

17:05 Protein structure evolution and convergence - Mathilde Carpentier (SU - MNH - CNRS)

17:30 Hybrid methods for analyzing conformational variability in cryo-EM and cryo-ET data - Slavica Jonic (CNRS & Sorbonne University, Paris)
17:55

17:55 - 20:00
Room: IBS building / lobby
Tuesday, 13 February 2024
08:10 Chair: Frédéric Cazals
Chair: Frédéric Cazals
08:10 - 09:50
Room: IBS seminar room
Contributions

08:10 Generative models and analysis tools for the study of highly-flexible (intrinsically disordered) proteins - Juan Cortés (LAAS-CNRS)

08:35 Dissecting peripheral protein-membrane interfaces - Nathalie Reuter (University of Bergen)

09:00 Spectral partitioning into protein structural domains - Edoardo Sarti (Inria)

09:25 Integrative structure of a histone chaperone-histone complex - Hugo van Ingen (Utrecht University)
09:50 Coffee Break
Coffee Break
09:50 - 10:20
Room: IBS building / lobby
10:20 Chair: Juan Cortès
Chair: Juan Cortès
10:20 - 12:00
Room: IBS seminar room
Contributions

10:20 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 Integrative spatiotemporal map of nucleocytoplasmic transport - Barak Raveh (Hebrew University of Jerusalem)

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

11:35 Asymmetric hydrophobic mismatch in assembly of ATP synthase rotor ring - Ivan Gushchin (Moscow Institute of Physics and Technology)
12:00 Lunch
Lunch
12:00 - 13:45
13:45 Chair: Monste Soler-Lopez
Chair: Monste Soler-Lopez
13:45 - 15:25
Room: IBS seminar room
Contributions

13:45 Integrative ensemble modeling that utilizes distance distribution restraints - Gunnar Jeschke (ETH Zürich)

14:10 Mechanistic study of MexAB-OprM efflux pump by an integrative approach - Isabelle Broutin (université Paris Cité)

14:35 Challenges in visualizing structural flexibility of the SAGA complex - Gabor Papai (INSERM)

15:00 Deciphering protein conformational dynamics with cryo-EM and MD simulations - Rémi Vuillemot (LJK, Université Grenoble Alpes, France)
15:25 Coffee break
Coffee break
15:25 - 15:55
Room: IBS building / lobby
15:55 Chair: Matin Weik
Chair: Matin Weik
15:55 - 17:10
Room: IBS seminar room
Contributions

15:55 Mariage of Cryo-EM, Solution Scattering, and Computational Science - Masaaki Sugiyama (Kyoto University, Institute for Integrated Radiation and Nuclear Science)

16:20 Protein Dynamics at extreme Temperatures - Beatrice CAVIGLIA (Universite' Paris Cite', University of Perugia)

16:45 POU5F1B and GOLPH3, two challenging proteins in structural biology - Maria Marcaida (EPFL)
17:10 Coffee break
Coffee break
17:10 - 17:40
Room: IBS building / lobby
17:40 Chair: Gunnar Jeschke
Chair: Gunnar Jeschke
17:40 - 18:55
Room: IBS seminar room
Contributions

17:40 Integrative structural biology of cell extracts : an application to structurally undercharacterized organisms - Ambroise Desfosses (CNRS- IBS)

18:05 Ensemble based calculations of spin-spin couplings in proteins: from ordered to disordered peptides - Amina Gaffour

18:30 Hinge disulfides in human IgG2 CD40 antibodies modulate receptor signaling by regulation of conformation and flexibility - Hayden FISHER (ESRF)
18:55 Free evening
Free evening
18:55 - 20:00
Wednesday, 14 February 2024
08:30 Chair: Martin Blackledge
Chair: Martin Blackledge
08:30 - 09:45
Room: IBS seminar room
Contributions

08:30 Intrinsically disordered regulators of endocytosis - an integrated NMR/single molecule fluorescence approach - Sigrid Milles (Forschungsverbund Berlin e.V. (FMP))

08:55 The Influence of Globular Domains on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation - Michael Bakker (Charles University)

09:20 Integrative Biology to tackle mitochondrial respiration in Alzheimer’s pathogenesis - Montserrat Soler Lopez (ESRF)
09:45 Coffee Break
Coffee Break
09:45 - 10:15
Room: IBS building / lobby
10:15 Chair: Sigrid Milles
Chair: Sigrid Milles
10:15 - 11:30
Room: IBS seminar room
Contributions

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

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

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

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

12:30 Lunch
Lunch
12:30 - 14:00

14:00

14:00 - 14:15
Room: IBS seminar room
14:15
14:15 - 15:30
Room: IBS seminar room
Contributions

14:15 CAPRI 2024: Pre- and post-Alphafold protein docking - Marc Lensink (CNRS)

15:00 Integrated pipeline for protein docking with extended and enhanced Alphafold-based modeling methods - Daisuke Kihara (Purdue University)
15:30 Coffee Break + posters
Coffee Break + posters
15:30 - 16:15
Room: IBS building / lobby
16:15
16:15 - 18:15
Room: IBS seminar room
Contributions

16:15 Towards integrative use of pyDock and AI-based modeling in 8th CAPRI - Juan Fernandez-Recio (ICVV-CSIC and BSC)

16:45 Prediction and refinement of protein assemblies with ClusPro, Alphafold and Molecular Dynamics. - Dima Kozakov (Stony Brook University)

17:15 MassiveFold: optimized massive sampling with AlphaFold2 - Guillaume Brysbaert (CNRS University of Lille)

17:45 From Interaction Prediction to Sequence Design: Unveiling PeSTo's Potential in Structural Biology - Lucien Krapp (Laboratory for Biomolecular Modeling, EPFL)
Thursday, 15 February 2024
09:00
09:00 - 10:30
Room: IBS seminar room
Contributions

09:00 Impact of AI-Based Modeling on the Accuracy of Protein Assembly Prediction: The CASP Perspective - Ezgi Karaca (Izmir Biomedicine and Genome Center, DEU)

09:30 What have we learned (and memorized) about peptide-mediated interactions in CAPRI and beyond? - Ora Schueler-Furman (Hebrew University of Jerusalem)

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

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

11:30 The Expanding Horizon of Protein Interactions - Shoshana Wodak (VIB-VUB Center doe Structural Biooogy, Brussels Belgium)
12:15 Lunch
Lunch
12:15 - 14:00
14:00
14:00 - 15:30
Room: IBS seminar room
Contributions

14:00 Multistage Docking Approach for Protein-RNA Interactions Prediction in CAPRI and CASP - Shan Chang (Jiangsu University of Technology)

14:30 An Iteratively Derived Knowledge-based Scoring Function at Atomic Level for Protein-DNA Complexes Evaluations - XIaoqin Zou (University of Missouri - Columbia)

15:00 FTDMP: a framework for protein-protein, protein-DNA and protein-RNA docking and scoring - Rita Banciul (Vilnius University) Justas Dapkunas (Vilnius University)
15:30 Coffee Break + posters
Coffee Break + posters
15:30 - 16:15
Room: IBS building / lobby
16:15
16:15 - 17:30
Room: IBS seminar room
Contributions

16:15 Interpretable Affinity Prediction and Generative Design for Protein-Ligand Interactions - Yang Shen (Texas A&M University)

16:45 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)
17:30

17:30 - 18:30
Room: IBS seminar room

19:30

19:30 - 22:30
Friday, 16 February 2024
09:00
09:00 - 10:00
Room: IBS seminar room
Contributions

09:00 Shape retrieval methods for the classification of protein surfaces - Grisell Diaz Leines (EMBL-EBI)

09:30 High-throughput prediction of ATP synthase rotor ring stoichiometries - Ivan Gushchin (Moscow Institute of Physics and Technology)
10:00 Coffee Break + posters
Coffee Break + posters
10:00 - 10:30
Room: IBS building / lobby
10:30
10:30 - 11:30
Room: IBS seminar room
Contributions

10:30 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 Modeling of immune recognition and protein complexes with deep learning and physics-based docking - Brian Pierce (University of Maryland)
11:30 Closure
Closure
11:30 - 12:00
Room: IBS seminar room

12:00 Lunch at the canteen
Lunch at the canteen
12:00 - 13:30