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Strasbourg Summer School in Chemoinformatics – 2024

University of Strasbourg, 24 – 28 June 2024

9th Edition of the CS3 – 2024

We are happy to announce the 9th Strasbourg Summer School in Chemoinformatics (CS3-2024) to be held in Strasbourg, France from June 24th to June 28th 2024.

CS3-2024 is a unique school mixing students, young and experienced scientists.

Due to overwhelming interest, we have reached our full capacity for attendees. We are sorry to announce that registration is now closed.

The program includes plenary lectures, poster session, oral presentations and hands-on tutorials. It covers the following topics :

  • Artificial Intelligence in chemistry
  • Big Data analysis and visualization
  • Chemical Reactions mining
  • New trends in QSAR modeling
  • Materials informatics
  • In silico pharmacology

Among invited speakers, it is our pleasure to acknowledge the participation of many world-class scientists :

  • Jürgen Bajorath (Univ. Bonn, Germany)
  • Thierry Langer (Univ. Vienna, Austria)
  • Gisbert Schneider (ETH, Zürich, Switzerland)
  • Artem Cherkasov (Univ. British Columbia, Canada)
  • Alexander Tropsha (Univ. North Carolina, Chappel Hill, USA)
  • Matthias Rarey (Univ. Hamburg, Germany)
  • Kimito Funatsu (NAIST, Japan)
  • Satoshi Maeda (Hokkaido Univ., Japan)
  • Jose Medina-Franco (Univ. Mexico)
  • Hanoch Senderowitz (Univ. Bar Ilan, Israel)
  • Connor Coley (MTI, USA)
  • Pavel POLISHCHUK (Palacky University, Olomouc, Czech Republic)
  • Olexandr Isayev (Carnegie Mellon Univ., USA)
  • Alessandra Roncaglioni (Inst. Mario Negri, Italy)

Registration form and contact

Due to overwhelming interest, we have reached our full capacity for attendees. We are sorry to announce that registration is now closed.

You can ask your questions by mail using this email address : chemoinfo-school@unistra.fr

Abstract Submission

Abstracts should be submitted to the Organizers by e-mail before April 15th 2024.
The attachment should be in RTF or DOC format.

e-mail : chemoinfo-school@unistra.fr

The posters should be of the following format : A0, Portrait orientation.

The abstract should be prepared according to a set of rules :
You can download the following word document to use as your abstract template.


Download abstract template

Here is an abstract example :

Communication Title (Arial, 14 pts, bold, centered)
FirstName LastName1, FirstNme LastNme1, FirstNme LastNme 2,… (Arial, 11 pts, centered)

1Laboratory1, University/Institute/Society…, Address, postal code, City, Country.
2Laboratory2, … (Arial, italics, 11 pts, aligned left)

Abstract Text : Arial, simple line spacing, 11 pts, justified

A black&white figure is authorized, referenced in the text as : (figure 1).
Figure legend in Arial, 8 pts, simple line spacing.

Bibliography :
[1] X.X ; Y.Y. J. Catal. 163 (2006) 192-156. (Arial, 10 pts, aligned left)

Please note that the abstract must not go beyond an A4 page (21 x 29,7 cm).
Margins are fixed to 2cm.

Conference fees

Early registration (before April 30th 2024)

Industrial 1000 €
Academics 700 €
Students 500 €
Accompagnying person 300 €
Pre-conference session : 250 €

After April 30th 2024

Industrial 1100 €
Academics 750 €
Students 550 €
Accompagnying person 350 €
Pre-conference session : 250 €

The registration fees covers :

Conference sessions and materials,
Conference dinner on 27 June,
Welcome party,
Coffee breaks,
Evening « Beer and Bretzel » parties on 26 and 27 June
Lunches on 25, 26 and 27 June
Cultural program on 27 June

Program of the School


The program includes plenary lectures, poster session, oral presentations and hands-on tutorials. It covers the following topics:

  • Artificial Intelligence in chemistry
  • Big Data in chemistry
  • Chemical Reactions mining
  • New trends in QSAR modeling
  • Material Informatics
  • In silico pharmacology
Chemoinformatics Strasbourg Summer School
(University of Strasbourg, 24 June - 28 June 2024)

Monday 24 June

14:00 - 16:40 Registration
16:45 - 17:00 Opening
17:00 - 18:00 Alex TROPSHA
University of North Carolina, USA
Reminiscing about the Future: New Trends in QSAR Modeling in the Age of Big Data, Generative AI, and Large Language Models
18:00 - 19:45 Welcome Party

Tuesday 25 June

09:00-09:40 Gisbert SCHNEIDER
ETH Zurich, Switzerland
De Novo Molecular Design with Machine Intelligence
09:40-10:20 Jürgen BAJORATH
University of Bonn, Germany
Language Models for Drug Design
10:20-10:40 coffee break
10:40-11:20 Kimito FUNATSU
NAIST, Japan
The Potential of Process Informatics
11:20-12:00 Matthias RAREY
University of Hamburg, Germany
News from the Outer Rim of Chemical Space
12:00-14:00 Lunch
14:00-14:20 Mikhail KABESHOV
AstraZeneca, Sodertalje, Sweden
AI tools for chemical synthesis and chemistry automation
14:20-14:40 Joao AIRES-de-SOUSA
New University of Lisbon, Caparica, Portugal
Exploring molecular heteroencoders with latent space arithmetic: atomic descriptors and molecular operators
14:40-15:00 Tagir AKHMETSHIN
University of Strasbourg, France
Construction of order-independent molecular fragments space with vector quantised graph autoencoder
15:00-17:00 Tutorial 1 –Gilles MARCOU
University of Strasbourg, France
Zooming chemical space with Generative Topographic Mapping
17:00-19:00 Poster session Beer & Bretzel

Wednesday 26 June

09:00-09:40 Thierry LANGER
University of Vienna, Austria
Next Generation Pharmacophore Modeling: Tools and Applications
09:40-10:20 Connor COLEY
MIT, Cambridge, USA
Balancing the design of molecular structures with the design of their syntheses
10:20-10:40 coffee break
10:40-11:20 José L. MEDINA-FRANCO
National Autonomous University of Mexico
Chemical space of food chemicals and natural products from Latin America
11:20-12:00 Alessandra RONCAGLIONI
Mario Negri Institute of Pharmacological Research, Milan, Italy
The use of QSAR in hazard assessment and (eco)toxicity for regulatory applications
12:00-14:00 Lunch
14:00-14:20 Yuliana ZABOLOTNA
Eli Lilly Company, Madrid, Spain
From chemical space visualization to strategic planning: leveraging chemography in drug discovery at Eli Lilly
14:20-14:40 Mireille KRIER
OpenEye, Cologne Germany
Detection of Cryptic Pockets for Drug Discovery
14:40-15:00 Marcus GASTREICH
BioSolveIT GmbH, St. Augustin, Germany
How Pharma Saves Tons Money: On-Demand Hits from Docking Ultralarge Spaces
15:00-17:00 Tutorial 2 – Esther KELLENBERGER/Luca CHIESA
University of Strasbourg, France
Protein structure prediction with AlphaFold2 for drug discover
17:00-19:00 Poster session Wine & Cheese

Thursday 27 June

09:00-09:40 Artem CHERKASOV
University of British Columbia, Canada
Integration of Deep Docking into Virtual Screening Workflow. The CACHE-1 Study Case
09:40-10:20 Satoshi MAEDA
Hokkaido University, Japan
Ab initio chemical reaction design and discovery through automated pathway exploration
10:20-10:40 coffee break
10:40-11:00 Anne-Claude CAMPROUX
Paris City University, France
Target IA and structural analysis protocol contribution to in silico drug design
11:00-11:20 Guilherme MARTINS SILVA
Harvard BIDMC, Boston, USA
Ultra-large virtual screens using fuzzy similarity, QSAR, docking, and molecular dynamics for multi-target anti-Alzheimer’s agents
11:20-11:40 Stefano PIERACCINI
University of Milan, Italy
Targeting the Todalam site on α-Tubulin: toward novel protein immobilization systems
11:40-12:00 Marco JUKIĆ
University of Maribor, Slovenia
Essential Steps in Protein-Ligand Preparation with Conserved Waters and Water Networks in Drug Design
12:00-14:00 Lunch
15:00-19:00 Cultural Program
19:00 Conference Dinner

Friday 28 July

09:00-09:40 Olexandr ISAYEV
Carnegie Mellon University, USA
Artificial Intelligence (AI) Solutions for Computational Chemistry and Organic Chemistry Tasks
09:40-10:20 Pavel POLISHCHUK
Palacky University, Olomouc, Czech Republic
Multi-instance learning as a response to the complexity of molecular entities
10:20-10:40 coffee break
10:40-11:20 Didier ROGNAN
Strasbourg University, France
Structure-based organic chemistry-driven ligand design from ultra-large chemical spaces
11:20-12:00 Hanoch SENDEROWITZ
Bar Ilan University, Israel
Materials Informatics for green energy harvesting and storage
12:00 Closure


Strasbourg Summer School - Strasbourg, France, 24 – 28 June 2024

Welcome to Strasbourg !

Its magnificent Cathedral, its fine food, "La Petite France" the typical quarter beloved of the tourists, not to mention the Grande-Ile, a UNESCO World Heritage site, have given it its reputation as a city anchored in History and Tradition.

Located in the "Esplanade" district, the Central Campus is near Strasbourg historical center. Also called "Esplanade Campus", it is the main University of Strasbourg Campus, regrouping University headquarters and many University of Strasbourg elements (including the "Tour de Chimie"), as well as the main part of the research units. Several independant high schools are present as well (Ecole Supérieure des Arts Décoratifs de Strasbourg and INSA).

Conference venue

The conference will be held at the European Doctoral College building in the central campus of the University of Strasbourg (46 Boulevard de la Victoire, 67000 Strasbourg).

Campus map

1 : European Doctoral College (46 Bd de la Victoire, 67000 Strasbourg)
2 : Chemistry Tower (1 Rue Blaise Pascal, 67008 Strasbourg)
3 : Restaurant "le 32" (Boulevard de la Victoire, Strasbourg)

How to get to the Conference Venue ?

From the airport

  • Take the shuttle train until the terminus Strasbourg Railway Station (see here)
  • Take the tram line C, direction "Neuhof Rodolphe Reuss" and get off at the stop "Observatoire".

From the train station

Take the tram line C, direction "Neuhof / Rodolphe Reuss" and get off at the stop "Observatoire".

From a bus or tram station

The Central Campus is situated near the tram station "Observatoire" on lines C and E.
Please check the map of the city network Here

You can buy tram tickets via the CTS application (Google Play, App Store), or at each tram station.

By car

Coming from the North, on highway A4:

  • Follow the directions to "Kehl".
  • After the tunnel, stay on the left and follow the direction "Esplanade".
  • Turn left and cross the Pont du Danube.
  • Go straight on Rue d’Ankara and on Rue de Leicester.
  • Turn left to rue de Londres.
  • At traffic light, go straight across avenue du General de Gaulle and the tram rails.
  • Enter the Place d’Athènes, which is in front of the Campus Central.

Coming from the South, on highway A35:

  • Take the Exit "Place de l’Etoile-Neudorf", stay on the left lane.
  • Follow the direction to Kehl.
  • Continue as described above (directions for coming from the North on highway A4).

Important information !

We would like to inform you that during the period from Monday, June 24th to Friday, August 23rd, 2024, inclusive, the tram company will be carrying out maintenance work on the tramway tracks. This will result in a complete interruption of service on the affected sections.

To ensure continuity of service, replacement buses will be put in place on the sections not served by the tramway during the same hours of operation.

Trams C and E are not running between Esplanade and Landsberg stations.

The northbound Tram C runs only between Gare Centrale and Esplanade.

The northbound Tram E runs only between Robertsau L’Escale and Esplanade.

The southbound Trams C and E are exceptionally running only between Campus d’Illkirch and Neuhof Rodolphe Reuss (with a route change at Landsberg).

Tram D is operating normally.

The map of the central campus is available here.

Photos by Jonathan Martz and Geneviève Engel.

Social events

Social program map

The social program is a boat visit of the City. Here is the map to go to the port.

Conference dinner map

1 : European Doctoral College (46 Bd de la Victoire, 67000 Strasbourg)
2 : Restaurant "la Bourse" (Place du Maréchal de Lattre de Tassigny, Strasbourg)

Crash Course

Crash Course in Chemoinformatics
Monday, 24th of June 2024
4th floor of the Faculty of Chemistry building (1 rue Blaise Pascal)
University of Strasbourg

08h30-09h30 Dragos Horvath Introduction to Chemoinformatics
09h30-10h30 Gilles Marcou Machine Learning
10h30-10h50 Coffee break
10h50-12h30 Tutorial (Gilles Marcou) QSAR Tutorial
Introduction to data mining slides
12h30-14h00 Lunch (Restaurant “32” on campus)
14h00-15h00 Esther Kellenberger Structure-based ligand discovery
15h00-16h00 Tutorial (Esther Kellenberger, Dragos Horvath, Gilles Marcou) Docking
16h00 Go to the conference registration and opening ceremony


ID Speaker Title
1 Philippe GANTZER Chemography-Guided Analysis of Reaction Path Networks by GTM
2 Jean-François AYME Cooperative Mobile Robots for Autonomous Synthetic Chemistry
3 Iryna BOIKO Machine Learning Models for Yield Predictions of Biginelli Reaction
4 Tarik BOUMAZA A Multi-Scale Chemical Reaction Database Visualisation
5 Colin BOURNEZ Functional group switching: harnessing the power of bioisosterism strategies in drug design
6 Leonard BUI Curation and Evaluation of an In-House Virtual Compound Library: Comparative Analysis with Commercial Collections and Synthetic Feasibility Assessment
7 Guillaume CHARIFI-HOAREAU Optimization of small molecule inhibitors targeting the SIRPɑ-CD47
immune checkpoint
8 Luca CHIESA Function-based virtual screening using machine learning and single
ligand dynamic interaction data
9 Côme GHADI Rational design of new DltB inhibitors
10 Teodora DJIKIC-STOJSIC The IMS Library: an in-House Collection Based on Chemical Diversity, Scaffold Novelty and Synthetic Accessibility
11 Nemanja DJOKOVIC Integrative Framework for Developing Innovative SIRT2 Inhibitors
12 Nico DOMSCHKE Modeling of Complex Chemical Reaction Networks
13 Valeriia FIL Beyond Validity and Novelty: Scaffold-based Metrics for Evaluating Chemical Structure Generators
14 Daniel FOIL Characterization of the Chemical Space of Genotoxicity Databases in Comparison to Pesticides and their Metabolites
15 Hosein FOOLADI Quantifying the hardness of bioactivity prediction tasks for transfer learning
16 Jozef FÜLÖP Cheminformatics Analysis of RNA-Binding Ligands
17 Sahil GAHLAWAT Predictive model for the Ir-catalyzed hydrogen isotope exchange reaction
18 Remi GOJARD New Insights on the structural features of Apis Mellifera Nicotinic Acetylcholine Receptors
19 Tobias HARREN DoGSite3 Scorer: Explainable Binding Site Druggability Predictions
20 Roxane JACOB Graph Neural Network Model with Uncertainty Estimation for the Prediction of Xenobiotic Sites of Metabolism
21 Christian JELSCH Mapping the favourable character of intermolecular contacts by electrostatic fingerprints
22 Dina KHAZANOVA Benchmarking of GPCR AlphaFold models
23 Vladimir KOZYREV Active learning to select the most suitable reactants for synthesizing target-specific ligands
24 Ariadna LLOP PEIRO PDB-CAT: Classification and Analysis Tool for PDB files
25 Pablo MAS Enhanced Molecule Selection via Active Learning in Lead Optimization for Drug Discovery
26 Matthieu MONTES VTX: High-performance molecular structure and dynamics visualization software
27 Karina PIKALYOVA Design of highly potent anti-biofilm, antimicrobial peptides using explainable artificial intelligence
28 Regina PIKALYOVA CoLiNN: Enabling Rapid Visualization of DNA-Encoded Libraries Without Compound Enumeration
29 Louis PLYER Implementation of soft grading systems for chemistry in a Moodle plugin.
30 Bryan RENARD De novo generation of peptide binders using Protein Large Language Models: towards anti-obesity bioactive peptides
31 Daniel ROSE PhectorMatch: Contrastive Learning Enables Fast Virtual Screening with 3D Pharmacophore Models
32 Zeined SI CHAIB Exploring Large Chemical Spaces for Lead Optimization
33 François SINDT Protein Structure-Based Organic Chemistry-Driven Ligand Design from Ultralarge Chemical Spaces
34 Filip SZCZYPINSKI Exploration of the polymorphic solid-state landscape of an amidelinked organic cage using low-cost computation and automation
35 Sara TANOVIC Probing the Generalisability of Single-Step Retrosynthesis Models
36 Lauri URVAS Search for dimerization-biased ligands of CCR2: a novel approach to target an elusive receptor family
37 Thi NGOC LAN VU Can machine learning-based docking approaches outperform or complement classical docking approaches in virtual screening?
38 Wei-Chieh WANG Can active learning improve the performance of computational mass spectrometry? Case study on the example of ionization efficiency predictions
39 Pierre LLOMPART Transforming molecular optimization using collective intelligence
40 Pierre LLOMPART Drug absorption, a multi-task solution to a multi-parametric problem
41 Johanna GIOVANNINI How to illuminate the Dark Side of the Kinome
42 Sharon BRYANT The NeuroDeRisk In Silico Toolbox: De-Risking Neurotoxicity and 3D-Pharmacophores
43 Erik YEGHYAN The Freedom space - GTM based analysis of a new chemical space using ChemAtlas tool
44 Timur MADZHIDOV Enhancements in Modelling with Reaxys Reaction Data Tailored to AI and ML Applications



  • Alexandre VARNEK (Chairman) - University of Strasbourg, France
  • Gilles Marcou - University of Strasbourg, France
  • Dragos Horvath - National Center for Scientific Research (CNRS), France
  • Olga Klimchuk - University of Strasbourg, France
  • Fanny Bonachera - National Center for Scientific Research (CNRS), France