AI in Chemistry and Biology:
Evolution or Revolution?

Beilstein Bozen Symposium
2024

June 4–6, 2024

Hotel Jagdschloss Niederwald
Rüdesheim, Germany

 

Scientific Committee:

Tim Clark / Friedrich-Alexander-University Erlangen-Nürnberg

Antonella Di Pizio / Leibniz Institute for Food Systems Biology and Technical University Munich

Oliver Koch / University of Münster

Carsten Kettner / Beilstein-Institut

Overview

This symposium treated the impact of Artificial intelligence (AI) and Machine Learning (ML) on chemistry and biology, including drug design. The underlying theme of the discussions was what we can now do with AI and ML that we couldn’t do before. For instance, is AI simply a new interpolation method in the old traditional computer-aided drug design (CADD)? Are the methods applied nowadays unreliable in contrast to the those applied in the early days? How can we combine the development and application of new materials with AI-generated knowledgebases? How much can AI help in the prediction and retro-synthesis of new chemical compounds, and how useful are these compounds? Still, the quality of published data matters as meaningful AI applications depend on the availability of high-quality test datasets.

These and more questions have been addressed:

  • chemical sensing
  • chemical aided drug design
  • protein structure prediction
  • AI models from physical models
  • synthesis planning
  • human brain project
  • medical image recognition, and other interdisciplinary topics

In the tradition of the Bozen Symposia participants from widely differing areas of specialization presented provoking talks for a general but qualified scientific audience and researchers from the different disciplines came into contact and led to fruitful “out of the box” discussions.

Scientific Program

 

Tuesday, June 4

 

9:00
Welcome and Opening
Carsten Kettner

Session Chair: Oliver Koch

9:20
When Did Cheminformatics Become ML? [Slides]
Tim Clark, Friedrich-Alexander University Erlangen-Nürnberg

10:00
Evolution of the Chemical Space and the Role of AI in its Further Expansion [Slides]
Guillermo Restrepo, MPI for Mathematics in the Sciences, Leipzig

10:40
Lightning Talks

11:10
Coffee break and poster session

11:40
AI (R)evolution in Small Molecule Drug Design
Christian Kramer, Hoffmann-LaRoche, Basel

12:20
Also in Chemistry, Deep Learning Models Love Really Big Data [Slides]
Christoph Steinbeck, University of Jena

13:00
Lunch

Session Chair: Christoph Steinbeck

14:15
Software Lightning Talk

14:25
AI in Medicinal Chemistry: The Revolution yet to Unfold
Christian Tyrchan, AstraZeneca, Gothenburg

15:05
Extrapolation with Chemical Machine Learning
Johannes T. Margraf, University of Bayreuth

15:45
Coffee break and poster session

16:15
Should We Expect a Revolution from "Artificial" Intelligence?
Benjamin Risse, University of Münster

16:55
Machine Learning for Molecular Sensing [Slides]
Giovanni Cuniberti, Technical University Dresden

17:35
Opportunities of Shared AI Infrastructure in Chemistry Research
Beth A. Plale, Indiana University, Bloomington

18:15
Close

19:30
Dinner

 

 

Wednesday, June 5

 

9:00
Opening

Session chair: Tim Clark

9:05
AI in Drug Design - Let's Talk about Data
Oliver Koch, University of Münster

9:45
Drug Discovery and Repurposing in the LLM Era
Tudor Oprea, Expert Systems Inc., San Diego

10:25
Coffee break and poster session

11:00
Artificial Intelligence in Drug Discovery - Towards Virtual Drug Discovery
Gerard J.P. van Westen, Universiteit Leiden

11:40
Artificial Intelligence in Drug Discovery - From Model to Process, From Academic Publication to Decision Making [Slides]
Andreas Bender, Cambridge University/Pangea Bio

12:20
Hybrid AI and Open Source for Kinase-focused Drug Design
Andrea Volkamer, Saarland University, Saarbrücken

13:00
Lunch

14:00 - 17:30
Excursion

19:30
Dinner

 

Thursday, June 6

 

9:00
Opening

Session chair: Antonella Di Pizio

9:05
Ensuring Neural Networks Robustness: Problems and Opportunities [Slides]
Ekaterina Komendantskaya, University of Southampton

9:45
Conditional Protein Design with Unsupervised Language Models
Noelia Ferruz, Barcelona Institute of Molecular Biology (online)

10:25
Coffee break and poster session

10:55
Protein Design 2.0
Birte Höcker, University of Bayreuth

11:35
New AI Toolkits for Structural Biology: Opportunities and Limitations [Slides]
Stefan Arold, KAUST, Thuwal

12:15
Application of Artificial Intelligence (AI) and Computer Simulations in GPCR Research
Jana Selent, Hospital del Mar Medical Research Institute (IMIM) & Pompeu Fabra University, Barcelona

13:00
Lunch

Session chair: Beth A. Plale

14:15
Cheminformatics and Modelling of Flavour Molecular Systems: Applications and Limitations of AI
Antonella Di Pizio, Technical University Munich

14.55
Siimulation-based Inferecne for Biophysics
Pilar Cossio, Simons Foundation, New York (Online)

15:35
Coffee break

16:05
Assisting Sampling of Physical Systmes with Generative Models
Marylou Gabrié, École Polytechnique Paris

16:45
Summary - Quo Vadis AI in Chemistry and Biology?
Karl-Heinz Baringhaus, Sanofi-Aventis GmbH, Frankfurt

17:25
Closing Remarks
Carsten Kettner

19:30
Dinner

 

Posters


No. 1

Providing Machine Learning Models for Property Predicition for Research Partners
Conrad Stork, BASF, Ludwigshafen

No. 2

Thyroid Ultrasound: Diagnostic Criteria and Artificial Intelligence Techniques
Karima Bahmane, ENSA, Agadir

No. 3

Recurrent Neural Chemical Reaction Networks that Approximate Arbitrary Dynamics
Alexander Dack, Imperial College London

 


No. 4

You Can't Improve what You Don't Measure - Measuring ML/AI Impact in Drug Discovery Projects
Christian Herhaus, Merck KGaA, Darmstadt

No. 5

Machine-learning Assisted ReaxFF Simulations for Accurate Computational pKa Estimations of Organic Molecules
Filip Sagan, Jagiellonian University, Krakow

No. 6

3D-QSAR Meets ML for Binding Affinity Prediction
Katarina Stanciaková, OpenEye, Cologne

No. 7

Efficient Torsion Scans of Small Molecules with TRIP SE(3) Transformer and the ZONTAL Platform
Dennis Della Corte, ZONTAL Inc., Provo

Impressions

Jagdschloss Niederwald
Conference Photo
Stefan Arold
Audience 1
Andreas Bender
Audience 2
Tim Clark
Giovanni Cuniberti
Andrea Volkamer
Karl-Heinz Baringhaus
Antonella Di Pizio
Noelia Ferruz
Marylou Gabrie
Birte Höcker
Tudor Oprea
Johannes Margraf
Benjamin Risse
Beth Plale
Jana Selent
Guillermo Restrepo
Christoph Steinbeck
Christian Kramer
Christian Tyrchan
Exkursion 1
Exkursion 2
Exkursion Engel 1
Exkursion Engel 2
Exkursion Engel 4
Exkursion Engel 5
Exkursion Zielesny
Ekaterina Komendantskaya
Oliver Koch
Dennis Della Corte
Gerard Van Westen
Closing Remarks