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Strasbourg Summer School in Chemoinformatics - 2018

Chemoinformatics Strasbourg Summer School, Strasbourg 2018

Chemoinformatics Strasbourg Summer School 2018

University of Strasbourg, 25 June - 29 June 2018

The following topics are suggested for the scientific program:

  • Big Data in Chemistry
  • In silico pharmacology
  • Material Informatics
  • Text mining in chemistry
  • Virtual screening techniques
  • Deep learning
  • Data analysis and visualization

This event is organised with the support of:

  • the French Society on Chemoinformatics (SFCi, Société Française de Chemoinformatique)
  • the GDR Chémoinformatique (CNRS)
  • the University of Strasbourg
  • the Franco-German University

The opening lecture will be given by Prof. Jean-Pierre Sauvage, Nobel Prize laureate (University of Strasbourg).

Confirmed lecturers:

J.-P. Sauvage (University of Strasbourg, France)
J. Bajorath (University of Bonn, Germany),
K. Funatsu (Tokyo University, Japan),
T. Langer (University of Vienna, Austria),
M. Rarey (University of Hamburg, Germany),
G. Schneider (ETH, Zürich, Switzerland),
C. Sotriffer (University of Würzburg, Germany),
I. Tetko (Helmholtz Zentrum München, Germany),
A. Tropsha (University of North Carolina at Chapel Hill, USA)
X. Morelli (Université Aix-Marseille, France)
C. Hongming (AstraZeneca Gothenburg, Sweden)
I. Baskin (Lomonosov University of Moscow, Russia)
H. Senderowitz (Univ. Bar Ilan, Israel)
A. Cherkasov (University of British Columbia, Vancouver, Canada)
P. Ertl (Novartis, Basel, Switzerland)

Tiny URL of this page: http://tiny.cc/CS3-2018
QR code:

Pre-conference events

Monday 25th June 2018 (University of Strasbourg): Crash course in Chemoinformatics (lectures and tutorials).

Post-conference event

Monday 2d of July and Tuesday 3rd of July 2018 (University of Strasbourg): 7th French-Japanese Workshop on Computational Methods in Chemistry

Dedicated to the memory of Professor Toshio Fujita

Organizers : A. Varnek, D. Rognan (France) and K. Funatsu (Japan)



  • Alexandre VARNEK (Chairman) - University of Strasbourg, France
  • Didier ROGNAN - National Center for Scientific Research (CNRS), France
  • Esther Kellenberger - 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

Informations about Strasbourg University


Strasbourg Summer School - Strasbourg, France, 25 June - 29 June 2018

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).

How to register

no publication

Abstract submission

Strasbourg Summer School - Strasbourg, France, 25 June - 29 June 2018

Abstracts should be submitted to the Organizers by e-mail before April 15th 2018.
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.

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 fee

Strasbourg Summer School - Strasbourg, France, 25 June - 29 June 2018
  • Early registration (before April 15th 2018) :
Industrial 950 €
Academics 650 €
Students 450 €
Accompagnying person 300 €
  • After April 15th 2018 :
Industrial 1000 €
Academics 700 €
Students 500 €
Accompagnying person 350 €
  • Pre-conference session: 250 €

The registration fees covers :

  • Congress materials,
  • Conference dinner,
  • Welcome party,
  • Coffee breaks,
  • Evening beer parties on 26 and 27 June
  • Lunches on 26, 27 and 28 June
  • Cultural program
  • Public transportation

Registration form and contact

Online registration

Registrations are closed.


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

Program of the School


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

  • Big Data in chemistry
  • Material Informatics
  • Machine-Learning methods
  • Virtual screening techniques
  • In silico pharmacology
Chemoinformatics Strasbourg Summer School
(Université de Strasbourg, 25 - 29 juin 2018)

Monday 25 June

13:30-16:30 Registration  
9:00-16:15 Preconference session “Introduction into Chemoinformatics” (for registered persons only)  
14:00-16:00 Workshop Shrödinger  
14:00-16:00 Workshop Inte:Ligand  
16:30-17:00 Opening  
17:00-18:00 Jean-Pierre SAUVAGE From Interlocking and Knotted Rings to Molecular Machines abstract
18:00-19:45 Welcome Party  

Tuesday 26 June

9:00-9:40 Jürgen BAJORATH Emerging Big Data: Chemoinformatics-Driven View of Kinase Drug Discovery abstract slides
9:40-10:20 Hongming CHEN Cheminformatics in Drug Discovery, an Industrial Perspective abstract slides
10:20-10:40 coffee break
10:40-11:20 Xavier MORELLI Integrated Strategy for Lead Optimization based on fragment growing: The DOTS (Diversity Oriented Target-focused Synthesis) approach abstract slides
11:20-12:00 Igor TETKO The best practices of multilearning for (Big) data analysis abstract slides
12:00-14:00 Lunch
14:00-14:20 Sharon D. BRYANT Elegant Methods for Drug Discovery Research Using Advanced 3D-Chemical Feature Based Pharmacopohores & LigandScout abstract slides
14:20-14:40 David RINALDO Conformational Sampling and Binding Affinity Prediction of Macrocycles abstract slides
14:40-15:00 Manabu SUGIMOTO Electronic-Structure Informatics Combined with Linguistic Descriptions abstract slides
15:00-17:00 Tutorial 1 – Gilles MARCOU Data visualization, analysis and modeling using Generated Topographic Mapping slides
17:00-19:00 Poster session Beer & Bretzel

Wednesday 27 June

9:00-9:40 Alex TROPSHA Applications of machine learning and artificial intelligence to designing chemicals and materials with the desired properties abstract slides
9:40-10:20 Matthias RAREY Computational Methods for Cheminformatics and Structure-Based Design abstract slides
10:20-10:40 coffee break
10:40-11:20 Christoph SOTRIFFER Covalent ligands: Challenges and approaches for docking and design abstract slides
11:20-12:00 Kimito FUNATSU De novo structure generation using inverse QSAR approach abstract slides
12:00-14:00 Lunch
14:00-14:20 Thierry HANSER Applicability domain and confidence in predictions: Towards a more formal framework abstract slides
14:20-14:40 Timur MADZHIDOV State-of-the-Art in Chemical Reaction Characteristics Prediction Using Condensed Graph of Reaction abstract slides
14:40-15:00 Pavel POLISHCHUK HTS-likeness: physicochemical parameters to create libraries abstract slides
15:00-17:00 Tutorial 2 – Esther KELLENBERGER Consensus binding motif applied to fragment docking
17:00-19:00   Beer & Knack

Thursday 28 June

9:00-9:40 Gisbert SCHNEIDER Artificially-intelligent drug design abstract slides
9:40-10:20 Artem CHERKASOV Cheminformatics driven development of novel therapies for drug resistant prostate cancer abstract slides
10:20-10:40 coffee break
10:40-11:00 J.B. BROWN Why adaptively-built simple models using small datasets can be sufficient for chemical modeling abstract slides
11:00-11:20 Alessandro SANGION A Tiered Approach for Screening Chemicals for Biomagnification Potential in Humans abstract slides
11:20-11:40 Nathalie LAGARDE Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets abstract slides
11:40-12:00 Colin BOURNEZ Frags2Drugs: Discovery of new kinase inhibitors from 3D fragment network abstract slides
12:00-14:00 Lunch
15:00-19:00 Cultural Program
19:00 Conference Dinner

Friday 29 June

9:00-9:40 Hanoch SENDEROWITZ Molecular Dynamics Simulations: Theory and Applications in Drug Design abstract slides
9:40-10:20 Peter ERTL Machine learning applied to natural products - Lessons from Nature inspiring the design of new drugs abstract slides
10:20-10:40 coffee break
10:40-11:20 Igor BASKIN Deep learning: What makes neural networks great again? abstract slides
11:20-12:00 Thierry LANGER Adventures in Computer-Assisted Molecular Design abstract slides
12:00 Closure

Pre-conference events

Crash course in Chemoinformatics

You shall download datasets and instructions.

The software are pre-installed in the computer room, but they are available for free and request here: http://infochim.u-strasbg.fr/spip.php?rubrique41

Posters and Abstracts

Strasbourg Summer School - Strasbourg, France, 25 June - 29 June 2018
ID Speaker Title
P1 Arina AFANASYEVA Combination of structure-based and machine learning approaches for developing of selective kinase inhibitors
P2 Valentina AFONINA Ranking of Reaction Condition Applicability Based of Artificial Networks
P3 Francois BERENGER Combining a bisector tree with the Tanimoto distance for similarity searches and beyond
P4 Caroline BUSHDID Agonists of G protein coupled-odorant receptors are predicted from chemical features
P5 Yuliana ZABOLOTNA Generative Topographic Mapping in Virtual Screening: why ensemble of maps is needed?
P6 Loïc DREANO A relational database structure for fast and efficient mining of molecular interactions in the PDB
P7 Eddy ELISEE Molecular dynamics studies of the variability of ZN-coordination sphere in metallo-β-lactamases.
P8 Héléna A. GASPAR Drug Targetor – Prioritizing Drugs and Targets Using Genetics
P9 Timur GIMADIEV Reaction data treatment by means of Condensed graph of reaction
P10 Marta GLAVATSKIKH Modeling of complex reaction data: the case of tautomeric equilibria
P11 Priscila da S. F. C. GOMES Rescoring docking poses by graph matching of protein–ligand interactions: lessons learned from the D3R Grand Challenges
P12 Evgeni GRAZHDANKIN Developing probabilistic restraint optimization protocols for comparative modelling in MODELLER
P13 Takafumi INOUE Similarity Analysis on Fatty Acid Synthase Inhibitors Based on Three-Dimensional Electronic Descriptors
P14 Célien JACQUEMARD Fragment docking: Pose selection by consensus references binding mode
P15 Swarit JASIAL How Frequently Are Pan-Assay Interference Compounds Active?
P16 Kyrylo KLIMENKO R-based application for a pairwise SAR analysis
P17 Florian KOENSGEN Discrimination of G–protein coupled receptors and their conformational states using intramolecular interaction
P18 Ashenafi LEGEHAR IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data
P19 Yulia D. LOGINOVA The Donor-Acceptor Dichotomy of Isocyanides as Stereoelectronic Chameleons in Radical Additions
P20 Mariia MATVEIEVA Interpretation of QSAR models learned from imbalanced data
P21 Filip MILJKOVIC Exploring Selectivity of Multi-kinase Inhibitors across the Human Kinome
P22 Ikumi MORIKAWA Prediction and Search for Biogenic Amine Receptor Antagonists Based on Electronic-Structure Informatics
P23 Anastasia NIKITINA Virtual screening of small molecule libraries based on antiviral chemical space analysis
P24 Ramil NUGMANOV On-line reaction database cartridge with built-in condensed graph of reaction-based search engine
P25 Sebastian ODDSSON Natural product compound databases. Diversity and applicability analysis for Virtual Screening
P26 Boris SATTAROV Deep Learning and Generative Topographic Mapping tandem in de novo design of biologically active compounds
P27 Melanie SCHNEIDER Improving ligand screening by exploiting structure ensembles and machine learning
P28 Grzegorz SKORACZYŃSKI Predicting likelihood of organic molecules by structure based Markov random field
P29 Conrad STORK Hit Dexter 2.0: An In Silico Tool for Identifying and Analyzing Frequent Hitters
P30 Viet-Khoa TRAN-NGUYEN Generation and virtual screening of protein-based cavity pharmacophores: A prospective study
P31 Anne TROMELIN Identifying specific binding modes for the ligands of a multi-site GPCR by a 3D-QSAR pharmacophore approach
P32 Filippo LUNGHINI, Philippe GANTZER New QSAR Models Concerning (Eco)Toxicological Endpoints: Acute toxicity, Bioaccumulation and Biodegradability
P33 Pavel POLISHCHUK, Alina KUTLUSHINA Using a new 3D pharmacophore presentation for ligand-based modeling
P34 Alex NYPORKO Free energy profiles of DNA Pol II interaction with matrix-complimentary/non-complimentary nucleotides – umbrella sampling approach
P35 Omer KASPI Visualization of the Photovoltaic Space by Dimension Reduction Methods
P36 William BORT Generative Topographic Mapping for chemical reactions analysis: Evolution of the reaction space between 1976 and 2016
P37 J.B. BROWN Machine learning in drug discovery - are you evaluating your results fairly?
P38 Arkadii LIN Generative Topographic Mapping approach as a Virtual Screening tool: a benchmarking study
P39 Guillaume BECK Search of new inhibitors of PI3Kδ
P40 Thierry Hanser Applicability domain and confidence in predictions : Towards a more formal framework

Sponsors of the event


6th Chemoinformatics Strasbourg Summer School - Strasbourg, France, 25 June - 29 June 2018
Logo FRC
Logo of the foundation of the International Center for Frontier Research in Chemistry

Where to find accomodation during the conference


Strasbourg Summer School - Strasbourg, France, 25 June - 29 June 2018

Accomodation - Here is an non-exhaustive list of nearby hotels

Hotel Esplanade Strasbourg ✯✯
1,boulevard Leblois

Tél. +33 3 88 61 38 95
Fax. +33 3 88 60 66 87

Room rates from 47 to 70 €
Breakfast : 8€

Website : http://www.hotel-esplanade.fr/
Email : info@hotel-esplanade.fr

Hôtel aux trois roses ✯✯
7, rue de Zurich

Tél. +33 3 88 36 56 95
Fax. +33 3 88 35 06 14

Room rates from 55 to 95€
Breakfast : 8,50€
Sauna (only for clients): 5 (one person) – 8 (two persons)

Website : http://www.hotel3roses-strasbourg.com/
Email : info@hotel3roses-strasbourg.com

Hôtel de L’Ill ✯✯
8 Rue Des Bateliers

Tél. +33 3 88 36 20 01
Fax. +33 3 88 35 30 03

Room rates from 65 to 102€
Breakfast : 7,50€

Website : http://www.hotel-ill.fr/
Email : info@hotel-ill.com

Hôtel Suisse ✯✯
2/4 rue de la Râpe

Tél. +33 3 88 35 22 11
Fax. +33 3 88 25 74 23

Room rates from 68 to 135€
Breakfast : 10,90€

Website : www.hotel-suisse.com
Email : info@hotel-suisse.com

Hôtel des Arts ✯✯
10, place du Marché aux cochons de Lait

Tél. +33 3 88 37 98 37
Fax. +33 3 88 37 98 97

Room rates from 90 to 115€
Breakfast : 6,50€

Website : www.hotel-arts.com
Email : info@hotel-arts.com

Hôtel Gutenberg ✯✯
31, rue des serruriers

Tél. +33 3 88 32 17 15
Fax. +33 3 88 75 76 67

Room rates from 85 to 165€
Breakfast : 10€

Website : http://www.hotel-gutenberg.com/
Email : info@hotel-gutenberg.com

Hôtel des Anges ✯✯
48 rue du Vieux Marché aux Poissons

Tél. +33 3 88 32 47 38

Room rates from 69 to 119€

Website : www.hotel-des-anges.fr
Email : contact@hotel-des-anges.fr

Hôtel de la cruche d’or ✯✯
4-6 rue des Tonneliers

Tél. +33 3 88 32 11 23

Room rates from 75€

Website : https://www.booking.com/hotel/fr/la-cruche-d-or.fr.html

Hôtel de la Cathédrale ✯✯✯
12,13 place de la cathédrale

Tél. +33 3 88 22 12 12
Fax. +33 3 88 37 98 97

Room rates from 90 to 200€
Breakfast : 6,50€

Website : www.hotel-cathedrale.fr
Email : booking@hotel-cathedrale.fr

hôtel du dragon
Picture of the hotel du Dragon in Strasbourg

Hôtel du Dragon ✯✯✯
12 rue du Dragon

Tél. +33 (0)3 88 35 79 80

Room rates from 89 to 129€
Breakfast : 12€

Website : http://www.dragon.fr/chambres.aspx
Email : hotel@dragon.fr

Hôtel Diana Dauphine ✯✯✯
30 Rue de la 1ère Armée

Tél. +33 3 88 36 26 61
Fax. +33 3 88 35 50 07

Room rates from 89 to 215€
Breakfast : 12€

Website : www.hotel-diana-dauphine.com
Email : info@hotel-diana-dauphine.com

Hôtel Beaucour ✯✯✯
5, rue des Bouchers / 5, rue des Boeufs

Tél. +33 3 88 76 72 00
Fax. +33 3 88 76 72 60

Room rates from 62 to 123€
Breakfast : 13,50€

Website : http://www.hotel-beaucour.com/
Email : info@hotel-beaucour.com

Hôtel des Princes ✯✯✯
33, rue Geiler

Tél. +33 3 88 61 55 19
Fax. +33 3 88 41 10 92

Room rates from 110 to 135€
Breakfast : 13€
Bed and breakfast available for group of 20 people minimum : 45 to 75 € in double room.

Website : http://www.hotel-princes.com/
Email : princes@strasbourg.com

Hôtel Cardinal de Rohan ✯✯✯
17, rue du Maroquin

Tél. +33 3 88 32 85 11
Fax. +33 3 88 75 65 37

Room rates from 99 to 370€
Breakfast : 15€

Website : http://www.hotel-rohan.com/
Email : info@hotel-rohan.com

Hôtel Cour du Corbeau ✯✯✯✯
6-8 rue des Couples

Tél. +33 3 90 00 26 26
Fax. +33 3 90 00 26 36

Room rates starting from 168€
Breakfast : 13,50€

Website : http://www.cour-corbeau.com/
Email : H7575@accor.com

Hôtel Régent Petite France ✯✯✯✯✯
5 rue des Moulins

Tél. +33 3 88 76 43 43
Fax. +33 3 88 76 43 76

Room rates starting from 210€

Website : www.regent-petite-france.com/
Email : info@regent-petite-france.com

Hôtel Sofitel Strasbourg grande île ✯✯✯✯✯
4 Place Saint Pierre le Jeune

Tél. +33 3 88 15 49 15 / +33 3 88 15 49 00
Fax. +33 3 88 15 49 99

Room rates starting from 190€

Website : www.sofitel-strasbourg.com
Email : H0568@sofitel.com

Please check this pdf guide for more hotels recommendations as well as booking advice.

Tutorials of the school

no publication

Tutorial on Generative Topographic Mapping

The tutorial aims at presenting the Generative Topographic Mapping (GTM) algorithm [Bishop et al, Neural Computation 10, No. 1, 215–234 (1998)].

The GTM is an unsupervised method to map high dimensional data to a two-dimensional representation. In the process, the GTM builds a probabilistic model of the data that can be exploited for data characterization, comparison or classification and regression model building. The GTM approach will be used to analyze a dataset of flavors and to explore structure-flavor relationships. It will be the occasion to get some deeper insight into the method with a particular focus on the effects of the GTM parameterization on the obtained map.


The tutorial is based on three pieces of software:

  • xGTMapTool: a graphical user interface frontend for the preparation of a GTM.
  • xGTMview: an application to link the GTM trained on chemical data and the chemical structures.
  • xGTMmanifold: an application illustrating the concept of GTM manifold and data space.

The software are supplied on the USB key and can be downloaded for the OS of your choice:

  • Windows
  • Mac
  • Linux

Updated versions can be requested by contacting F. Bonachera

The licence of the software is distributed freely and a licence file, called «licence.dat» is distributed with the software for the OS of your choice (Windows, Mac or Linux).

The licence file must be installed in a proper location to be found.

  • On Windows: create the directory AppData\local\ISIDAGTM2018 directory at the root of your home directory and copy the file license.dat in it. The absolute path of the file should be similar to this one:


The file and the directory should have read and write permissions.

  • On Mac: create the directory .config/ISIDAGTM2018 directory at the root of your home directory and copy the file license.dat in it. The absolute path of the file should be similar to this one:


  • On Linux: create the directory .config/ISIDAGTM2018 directory at the root of your home directory and copy the file license.dat in it. The absolute path of the file should be similar to this one:



The tutorial uses a dataset of organoleptic compounds mined (in February 2018) from the FlavorDB database [Nucleic Acids Research, 2018, Vol. 46, Database issue].

The data are distributed on the USB key and can be downloaded here: http://infochim.u-strasbg.fr/CS3_2018/Tuto1/Data/FDB.zip

Step-by-step instructions

The protocol of the tutorial session is available in the following document: http://infochim.u-strasbg.fr/CS3_2018/Tuto1/Tutorial_GTM+DH_20_06_2018.pdf

Fragment docking: how to select the correct pose?

In this tutorial, we will use a novel knowledge-based method which is applicable to scoring of fragment docking poses.

The method, named LID for Local Interaction Density, builds a consensus interaction map from all experimental observations. All reference complexes are 3D-aligned in a common frame, then the density of interactions is encoded into a grid. Docking pose are scored from the matching of fragment atoms to the grid.

Here we asked whether information on binding mode can help selecting the correct pose of fragments docked into human carbonic anhydrase II (HCA II).


The complete tutorial material is available from the USB key. It can be downloaded also here: http://infochim.u-strasbg.fr/CS3_2018/Tuto2/lid_tutorial.zip

The archive uncompresses itself into a directory named lid_tutorial. The architecture of directories and files in this directory is important for the tutorial to work well.

Step-by-step instructions

The protocol of the tutorial session is available in the following document :





Credit photo : Petit Phil Photo