Programme Overview
1st and 2nd April 2025
Boothzaal M0.3, Mezzanine, University Library,
Utrecht Science Park, Heidelberglaan 3, Utrecht
Day 1 – April 1 | 13:00–18:00
Theme: Biomolecular Interactions & Conformational Dynamics
13:00 — Arrival & Poster Setup
13:15 — Keynote
Joost Schymkowitz (VIB-KU Leuven, Belgium)
Heterotypic Amyloid Interactions
13:45 — Flash Talks
Moritz Schäffler (Jülich Supercomputing Centre, Germany)
The Energy Landscape of Aβ42: A Funnel to Disorder for the Monomer Becomes a Folding Funnel for Self-Assembly
Victor Kyllesbech (Vrije Universiteit Amsterdam, Netherlands)
Tree-AMD: Exhaustive Molecular Dynamics for Ligand Egress Route Identification
Soroush Mozaffari (Maastricht University, Netherlands)
AI-Assisted Virtual Screening to Identify Novel PAD4 Inhibitors
Farzaneh Meimandi (Radboud University, Netherlands)
SwiftTCR: Efficient Computational Docking Protocol of TCRpMHC-I Complexes
14:45 — Coffee Break & Poster Session
15:15 — Keynote
Alexander Monzon (University of Padova, Italy)
Understanding the Sequence-Ensemble-Function Relationships of Intrinsically Disordered Proteins (IDPs)
15:45 — Flash Talks
Ida de Vries (Netherlands Cancer Institute)
Disentangling the CHAOS of Intrinsic Disorder in Human Proteins
Xiaotong Xu (Utrecht University, Netherlands)
Improved Structural Modelling of Antibodies and Their Complexes with Clustered Diffusion Ensembles
Dorothea Gobbo (Leiden University Medical Center, Netherlands)
From Disorder to Function: Probing the B-Domain of Coagulation Procofactors VIII and V via Molecular Dynamics
16:30 — Short Break
16:45 — Keynote
Alexandre Bonvin (Utrecht University, Netherlands)
More Than 20 Years of Integrative Modelling of Biomolecular Complexes – And Still Going Strong
17:15 — Flash Talks
Golnar Chapnevis (Vrije Universiteit Brussel, Belgium)
Molecular Determinants of Protein Resilience in Extremotolerant Organisms
Tugce Su Cobanoglu (Vrije Universiteit Amsterdam, Netherlands)
Lipid Detection in Parkinson’s Disease: Challenges in Lipidomics Analysis
17:45 — Closing Remarks
Day 2 – April 2 | 08:30–15:30
Theme: AI & Deep Learning in Structural Biology
08:30 — Breakfast & Coffee
09:00 — Keynotes
Erik Bekkers (University of Amsterdam, Netherlands)
Equivariance and Weight-Sharing in Neural Networks Without Specialized Modules
Chaitanya Joshi (University of Cambridge, United Kingdom)
All-Atom Diffusion Transformers: Unified Generative Modelling of Molecules and Materials
10:00 — Flash Talks
Friso de Kruiff (University of Amsterdam, Netherlands)
Generative Modeling and Representation Learning for Conformations and Sequence Data
Max Zhdanov (University of Amsterdam, Netherlands)
A Very Fast and Effective Point Cloud Architecture
10:30 — Coffee Break
10:45 — Flash Talks
Marieke Van Vreeswijk (Radboud University, Netherlands)
Latent Representations of Conformations and Energy Prediction
Daniel Alvarez (Netherlands Cancer Institute)
Tools to Label Sequence Motifs Involved in Binary Interactions
Konstantina Tzavella (Vrije Universiteit Brussel, Belgium)
D2D: A Constrained Foundation Model Applied to Predict the Impact of Mutations on Protein Stability and Function
11:30 — Lunch & Poster Session
13:00 — Keynotes
Giulia Crocioni (Netherlands eScience Center)
DeepRank2 and Its Application in Immunotherapy Design
Anton Feenstra (Vrije Universiteit Amsterdam, Netherlands)
PIPENN-EMB: Ensemble Net and Protein Embeddings Generalise Protein Interface Prediction Beyond Homology
13:50 — Flash Talks
Coos Baakman (Radboudumc, Netherlands)
SwiftMHC: A High-Speed Attention Network for MHC-Bound Peptide Identification and 3D Modeling
Ren Xie (Netherlands Cancer Institute)
LEGOFill: A Ligand–Protein Complex Hypotheses Generator
14:20 — Coffee Break
14:35 — Keynotes
Aalt-Jan van Dijk (University of Amsterdam, Netherlands)
Structure-Based Machine Learning to Predict Functional Specificity
Giacomo Janson (Michigan State University, United States)
Protein Dynamics
15:30 — Closing Remarks & Borrel