Final Programme overview Spring 2025 meeting
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
Spring 2025 meeting
Call for Abstracts
We welcome students and researchers at all career stages to submit abstracts for oral and poster presentations that integrate experimental methods, computational tools, and theoretical insights to advance the field.
While submitting an abstract is optional, registration is required for all attendees.
🗓 Abstract Deadline: March 15, 2025
📐 Length: ~300 words (including title, authors, affiliations)
📝 Register & Submit Here: Registration Link
Program Overview
Please note that you can register for either one day or both days.
Day 1 – April 1, 2025
Focus on structural analysis and methodologies beyond AI:
🔹 Conformational Dynamics – Explore biomolecular flexibility and conformational transitions.
🔹 Biomolecular Interactions – Discuss docking methodologies and tools for biomolecular binding.
🔹 Translational Applications – Discover how bioinformatics facilitates the development of targeted therapies.
Day 2 – April 2, 2025
Dedicated to AI-driven innovations in structural bioinformatics:
🔹 Deep Learning in Structural Biology – Cutting-edge AI techniques applied to biomolecular structures.
🔹 Structure-Based Property Prediction – AI-powered predictions of molecular interactions.
Event Details
📍 Venue: Boothzaal M0.3, Mezzanine, University Library Utrecht Science Park
💳 Registration Fee: Free for all participants
Why Attend?
✔ Gain insights from leading experts in bioinformatics and AI
✔ Present your research to an engaged scientific audience
✔ Network and foster multidisciplinary collaborations
✔ Enjoy a free, high-quality event
For inquiries, contact us at:
We look forward to welcoming you at NSBM Spring Meeting 2025!
NSBM Fall Meeting 2022 - Call for Abstracts and registration
Dear NSBM members and enthusiasts,
After a forced pause in our activities, we are very glad to announce that we will organize a next meeting. This year, the meeting will be organized together with our Belgian colleagues, in particular Prof Wim Vranken, of the ELIXIR Belgium node on the 27th of October 2022 and will be hosted in beautiful Brussels.
The current tentative programme is as follows:
Meeting Title: Structural bioinformatics beyond AlphaFold2
location: U-residence aan de Vrije Universiteit Brussel, VUB (Pleinlaan 2, B-1050 Brussels, Belgium)
We will host 3 sessions:
Session 1: 'Structural bioinformatics in the age of AlphaFold2' - Gert Vriend, Radboud University, the Netherlands
Session 2: ‘Large scale AlphaFold2 analyses’ - Christine Orengo, University College London, United Kingdom
Session 3: ‘Probabilistic approaches and representing conformational variability’ - Max Bonomi, Institut Pasteur, Paris, France
Session 4: ‘Proteomics & protein structure’ - Ron Heeren, M4I, Maastricht University, the Netherlands
Opening: 10:00 a.m.
Abstracts can be sent in via: https://easychair.org/cfp/NSBM2022
In line with the goals of the NSBM, we wish to provide a stage for Master students, PhD students, postdoctoral students and established researchers in any field of research connected to structural bioinformatics. There will be possibilities for oral and poster presentations, based on abstract selection by the organizing committee.
To enable a realistic planning of the meeting we ask participants to register via: https://bit.ly/nsbm2022
This meeting is made possible through the generous support of our sponsors:
The day will be informally closed by a beer&fries reception
Mark the date in your agendas!
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