Overview
A decade after AlphaGo’s landmark success, AlphaFold has transformed structural bioinformatics
from a search for static coordinates of protein atoms to a foundation for generative design. In
some way, one could say that the "folding problem" has been solved. Others may say it has evolved.
As the field moves beyond predictions of three-dimensional structures for isolated protein chains,
the frontier now lies in capturing the dynamic, multi-component reality of the cellular environment.
The workshop Structure of Biological Molecules is co-located with the
German Conference on Bioinformatics (GCB) 2026.
The workshop aims to connect ML researchers and structural biologists to discuss the current state
and perspectives of structural biology.
Call for Abstracts
We invite submissions of 1-page abstracts for 5-8 contributed talks and posters, presenting original research relevant to the workshop themes.
We welcome submissions on all topics related to structural bioinformatics, including but not limited to:
- Conformal landscapes:
Modeling protein dynamics and Boltzmann distributions.
- Genotype-to-phenotype relationships:
Predicting the effect of mutations on protein structure, dynamics, and function
- The non-folding frontier:
Predicting intrinsically disordered regions (IDRs) and transient states.
- Inter-molecular logic:
Protein-RNA interactions, ligand binding, and complex assemblies.
- Protein generation and design:
Models for de novo protein generation and targeted design.
Important Dates
All deadlines are 23:59 Anywhere on Earth (AoE).
| 06.08.2026 | Abstract submission deadline |
| 18.08.2026 | Notification of acceptance |
| 22.09.2026 | Workshop day |
Organising Committee
For general enquiries, contact the organisers at roman.joeres [AT] helmholtz-hips.de.
Author guidelines
The workshop is part of the German Conference on Bioinformatics (GCB) 2026. Therefore, participants and presenters must be registered for the GCB 2026. You can find more information about registration on the GCB 2026 registration page. For questions regarding registration or exceptions, please contact the workshop organisers at roman.joeres [AT] helmholtz-hips.de.
Submission Guidelines
The abstracts for this workshop follow the same requirements as for GCB 2026:
- 1-page abstract (including references and figures) in PDF format.
- Written in English.
- You can find a template from GCB here: Abstract Template
We encourage work submitted to GCB to be submitted to this workshop as well for presentation and discussion with a more specialized audience.
Programme
The workshop will run as a half-day event (12:30 to 16:45).
Session 1 - Chair: Olga Kalinina
| 12:30 | Opening Remarks |
| 12:40 | Dominik Grimm GraphXForm: graph transformer for computer-aided molecular design |
| 13:40 | Michael Backenköhler ChemICL: Uncertainty-Aware Bioactivity Modelling at Scale |
| 14:10 | Ashima Khanna Self-Improvement Imitation with Biologically Guided Search for Protein Design Under Oracle Budget |
| 14:30 | Coffee Break |
Session 2 - Chair: Volkhard Helms
| 15:00 | Roman Joeres Challenges in Enzyme-Small Molecule Interaction Prediction |
| 15:20 | Patrik Staak Machine Learning-based Modelling of FGF/FGFR Binding Affinity Unveils Limits of Quantitative Protein-Protein Interaction Prediction |
| 15:40 | Aram Papazian Predicting Context Specific Protein-Protein Interactions |
| eventually | Podium discussion |
| or | Mingle · Meet the speakers & Networking |
| Closing Remarks | |
| 17:00 | GCB Opening Keynote by Johannes Söding Protein structure searches in the era of AlphaFold and a new approach to phylogeny |
The Microsoft CMT service was used for managing the peer-reviewing process for this conference. This service was provided for free by Microsoft and they bore all expenses, including costs for Azure cloud services as well as for software development and support.