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Strasbourg Summer School in Chemoinformatics - 2016

Chemoinformatics Strasbourg Summer School, Strasbourg 2016

Chemoinformatics Strasbourg Summer School 2016

University of Strasbourg, 27 June - 1 July 2016

The following topics are suggested for the scientific program:

  • Data collections
  • Molecular similarity and diversity analysis
  • Molecular descriptors and molecular representations
  • Machine-learning methods in chemistry
  • Building and validating QSAR models
  • Virtual screening
  • In silico pharmacology

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


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

Confirmed speakers:

J. Bajorath (University of Bonn, Germany),
P. Bonnet (University of Orleans, France),
R. Lewis (Novartis, Basel, Switzerland) ,
M. Cecchini (University of Strasbourg, France),
A. Cherkasov (University of Vancouver, Canada),
K. Funatsu (Tokyo University, Japan),
R. Glen (University of Cambridge, UK),
T. Langer (University of Vienna, Austria),
K. Merz (Michigan State University, USA),
V. Poroikov (Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Russia),
M. Rarey (University of Hamburg, Germany),
G. Schneider (ETH, Zürich, Switzerland),
H. Senderovitz (Bar-Ilan University, Israel),
C. Sotriffer (University of Würzburg, Germany),
I. Tetko (Helmholtz Zentrum München, Germany),
A. Tropsha (University of North Carolina at Chapel Hill, USA),
J. Gasteiger (University of Erlangen, Germany)

Tiny URL of this page: http://tiny.cc/CS3-2016
QR code:

Pre-conference events

Monday 27th June 2016 (University of Strasbourg): Crash course in Chemoinformatics (lectures and tutorials).

Informations about Strasbourg University


Strasbourg Summer School - Strasbourg, France, 27 June - 1 July 2016

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 Location

The conference will be held in two locations :

  • The CDE (European College) : 46 boulevard de la Victoire 67000 STRASBOURG (Website)
  • The "Tour de Chimie" (Chemistry Tower - Faculty of Chemistry) : 1 rue blaise pascal 67000 STRASBOURG (Website)

These two buildings, both located in the Central Campus, are close to one another with an easy access :

CS3 2016 Location map
Location of the principal places of the CS3 2016 conference. The conference lectures are held in the CDE (2). Tutorials and events are accommodated into the Faculty of Chemistry (1). Both locations are near the tram station "Observatoire".

1 : Tour de Chimie (Chemistry Tower)
2 : CDE (European College)

How to get to the Central Campus - Esplanade?

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

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).

The map of the central campus is available here.

The European College can be found on number 40, and the Chemistry Tower on number 39.

Photos by Jonathan Martz and Geneviève Engel.

How to register

no publication

Abstracts submission

Strasbourg Summer School - Strasbourg, France, 27 June - 1 July 2016

Abstracts should be submitted to the Organizers by e-mail before April 15th 2016.
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, 27 June - 1 July 2016
  • Early registration (before April 15th 2016) :
Industrial 950 €
Academics 650 €
Students 450 €
Accompagnying person 300 €
  • After April 15th 2016 :
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 28 and 29 June
  • Lunches on 28, 29 and 30 June
  • Cultural program

Registration form and contact

Online registration

Registrations are closed.


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

Where to find accomodation during the conference


Strasbourg Summer School - Strasbourg, France, 27 June - 1 July 2016

Accomodation - 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 55 €
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 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


Program of the School


Strasbourg Summer School - Strasbourg, France, 27th June to 1st July 2016

Monday 27 June

9:00 - 17:00 Preconference session “Introduction into Chemoinformatics” Materials
16:00-18:00 Registration
18:00 - 18:10 Opening
18:10 - 19:10 Robert Glen (University of Cambridge, UK) Opening lecture From target validation to human studies: compound optimisation strategies abstract slides
19:15 - 21:00 Welcome Party

Tuesday 28 June

9:00 - 9:40 Johann Gasteiger (University of Erlangen, Germany) Explorations into Chemical Reactions and Biochemical Pathways abstract slides
9:40 - 10:20 Richard Lewis (Novartis, Basel, Switzerland) Building compound archives for the future abstract slides
10:20 - 10:40 coffee break
10:40 - 11:20 Jürgen Bajorath (University of Bonn, Germany) Analyzing Promiscuity at the Level of Active Compounds and Targets abstract slides
11:20 - 12:00 Kimito Funatsu (University of Tokyo, Japan) Soft Sensor: Chemoinfomatic Model for Efficient Control and Operation in Chemical Plants abstract slides
12:00-14:00 Lunch
14:00 - 14:20 Sharon D. Bryant (Inte:Ligand GmbH, Austria) 3D-Chemical Feature Based Pharmacophores: Essential Tools for Early Drug Discovery Research abstract slides
14:20 - 14:40 Daniel Alvarez-Garcia, (Discngine, France) Mining structural knowledge space for target profiling abstract slides
14:40 - 15:00 Marc C. Nicklaus (Naional Cancer Institute, USA) Tautomerism Databases abstract slides
15:00 - 17:00 Gilles Marcou (University of Strasbourg, France) Tutorial 1
17:00 - 19:00 Poster session Beer & Bretzel

Wednesday 29 June

9:00 - 9:40 Alex Tropsha (University of North Carolina, Chapel-Hill, USA) Computational Toxicology: Alarms about Chemical Alerts abstract slides
9:40 - 10:20 Christoph Sotriffer (University of Wuerzburg, Germany) Empirical scoring functions for affinity prediction of protein-ligand complexes abstract slides
10:20 - 10:40 coffee break
10:40 - 11:20 Gisbert Schneider (ETH, Zürich, Switzerland) Adaptive Molecular Design – Learning from Data abstract slides
11:20 - 12:00 Matthias Rarey (University of Hamburg, Germany) Computational Methods for Knowledge Extraction from Large Protein Structure Collections abstract slides
12:00-14:00 Lunch
14:00 - 14:20 David Rinaldo (Schrödinger GmbH, Germany) Diverse applications of free energy calculations in drug discovery abstract slides
14:20 - 14:40 Timur Madzhidov (Kazan Federal University, Russia) Assessment of optimal reaction conditions: deprotection in catalytic hydrogenation conditions abstract slides
14:40 - 15:00 Alban Lepailleur (University of Caen Basse-Normandie, France) Emerging patterns mining and automated detection of contrasting chemical features abstract slides
15:00 - 17:00 Esther Kellenberger (University of Strasbourg, France) Tutorial 2
17:00 - 19:00 Beer & Bretzel

Thursday 30 June

9:00 - 9:40 Thierry Langer (University of Vienna, Austria) Feature-based 3D Pharmacophores: The Current and The Future abstract slides
9:40 - 10:20 Artem Cherkasov (University of Vancouver, Canada) A Cheminformatics Story Behind 141,000,000$ Molecule abstract slides
10:20 - 10:40 coffee break
10:40 - 11:20 Kenneth Merz (Michigan State University, USA) Rapid Computation of Thermodynamic Quantities for Molecular Recognition Processes abstract slides
11:20 - 12:00 Hanoch Senderovicz (Bar Ilan University, Israel ) Material Informatics: Statistical Modeling in Material Sciences abstract slides
12:00-14:00 Lunch
14:00 - 19:00 Cultural Program
19:00 - 21:00 Conference Dinner

Friday 1 July

9:00 - 9:40 Pascal Bonnet (University of Orleans, France) Challenges and Successes in Using In Silico Tools in Kinase Research abstract slides
9:40 - 10:20 Marco Cecchini (University of Strasbourg, France) Computational Approaches to the Chemical Equilibrium Constant in Protein-Ligand Binding abstract slides
10:20 - 10:40 coffee break
10:40 - 11:20 Igor Tetko (Helmholz Institute, Neuherberg, Germany) Challenges and Opportunities for Big Data Analysis in Chemistry abstract slides
11:20 - 12:00 Vladimir Poroikov (Russian Academy of Sciences, Moscow, Russia) Drug Repurposing: New Uses for Old Drugs or Systems Biomedicine? abstract slides
12:00-14:00 Closure

Note for the members of the FSCi (French Society of Chemoinformatics): the great assembly (AG) will take place the Wednesday 29/06/2016 between 5pm and 6pm, after the tutorials. It will be located in the amphitheater used for the school.

Social program

A short description of the social and cultural events during the school.

Social events

In the evening, all participants are invited to social events, in order to give more time for exchanges, discussions and friendship.

  • Welcome party on 27/06
  • Beer&Bretzel on 28/06
  • Beer&Knack on 29/06
  • Conference dinner on 30/06, at the Caveau Lorentz-Klipfel in Barr
Conference diner at Caveau Lorentz-Klipfel
Conference diner at Caveau Lorentz-Klipfel in a previous CS3.
Olga Klimchuk

Conference dinner

The conference dinner will be held in the Caveau Lorentz-Klipfet in Barr. The dishes will be accompanied by degustation of Alsatian wines.

Caveau Lorentz-Klipfel
Alsacian wine in the Caveau Lorentz-Klipfel
Olga Klimchuk

Cultural event

On 30/06, before the conference dinner, all participants are invited to a tour in the beautiful medieval castle of Haut-Koenigsbourg, in the countryside of Strasbourg.

Haut-Koenigsbourg castle
View from the sky of the Haut-Koenigsbourg castle (by Jean-Luc Stadler)
Jean-Luc Stadler

Sponsors of the event


5th Chemoinformatics Strasbourg Summer School - Strasbourg, France, 27 June - 1 July 2016

Logo CDE
Logo of the Collège Doctoral Européen

Logo FRC
Logo of the foundation of the International Center for Frontier Research in Chemistry

Logo du programme Investissements d’Avenir, IDEX

Logo of the Labex Medalis

logo Discngine
Logo of the discngine company

logo BioSolveIT

Logo of ChemAxon
Logo ChemAxon 2016

Posters and abstracts 2016

Posters and abstracts

Strasbourg Summer School - Strasbourg, France, 27 June - 1 July 2016
ID Speaker Title
P1 Anighoro Andrew Introducing a hybrid virtual screening approach combining docking and binding mode similarity analysis
P2 Awuni Yaw Reduction of False Positives in Structure-Based Virtual Screening when Receptor Plasticity is Considered
P3 Berenger Francois Cluster Analysis of the NRLiSt BDB using ACPC
P4 Carles Fabrice Prediction of protein kinase-ligand interactions through 2.5D Proteochemometrics
P5 Dimova Dilyana Systematic generation of analog relationships of bioactive compounds and promiscuity analysis
P6 Dimova Dilyana Extraction of structure-activity relationship information from activity cliff clusters via matching molecular series
P7 Drwal Malgorzata Exploring the binding modes of fragments and their drug-like superstructures
P8 Ehret Jacques Role of chemicals in the onset of Diabetes Mellitus Type I and II
P9 Hoffer Laurent Diversity-Oriented Target-focused Synthesis (DOTS) : A hit optimization strategy combining molecular modeling and automated synthesis platform
P10 Kanev Georgi Protein family customised structural chemogenomics databases to investigate biomolecular interaction space
P11 Knehans Tim Molecular dynamics-based elucidation of neutraligand binding to chemokine CXCL12
P12 Koebel Mathew Mining chemical databases to obtain knowledge based information of non-covalent interactions
P13 Koensgen Florian CCR5 Dimer: Characterisation of Interface
P14 Lagarde Nathalie Discriminating agonist and antagonist ligands of the Nuclear Receptors using 3D pharmacophores
P15 Lepailleur Alban Detection of Structural Alerts for Toxic Side Effects. A Case Study on Mutagenicity
P16 Madzhidov Timur Assessment of optimal reaction conditions: deprotection in catalytic hydrogenation conditions
P17 Métivier Jean-Philippe Automated Generation of 2D-Pharmacophores from Large Datasets
P18 Nugmanov Ramil Workflow for reaction database cleaning and data standardization
P19 Polishchuk Pavlo Knowledge mining from chemical datasets based on interpretation of QSAR models
P20 Rastija Vesna Quantitative structure–activity relationship analysis for the antitumor activity of 3,4-ethylenedioxythiophene derivatives against six carcinoma cell lines
P21 Ratkova Ekaterina Cucurbit[n]urils as a test-system for an advanced in-silico docking
P22 Sasaki Shunta In silico identification of novel inhibitors of S6K1 kinase by SBDD and LBDD approach
P23 Šícho Martin Molpher-lib: software library for systematic chemical space exploration
P24 Skoraczynski Grzegorz Challenge of a priori classification of organic reaction yields and duration
P25 Trisciuzzi Daniela Docking-based classification models for estrogenic activity prioritization based on high-quality experimental data
P26 Tromelin Anne Pharmacophore Study of a Blending six-Component Odor Mixture
P27 Kayastha Shilva Visualization of multi-property landscapes for compound selection and optimization
P28 Beck Guillaume QSPR Modelling of new electrolytes
P29 Evenseth Linn Mari Structure, function and ligand interactions of the ecdysone receptor from Daphnia magna
P30 Freyd Thibaud Allosteric modulation of the human GABAB receptor
P31 Dehaen Wim Computer aided drug design towards new inhibitors of Kynurenine Aminotransferase
P32 Klimenko Kyrylo Chemical space of antiviral compounds: an analysis of the structure-activity information for compounds with antiviral activity from the ChEMBL database
P33 Rinaldo David Diverse applications of free energy calculations in drug discovery
P34 Subhash M Agarwal Development of QSAR classification models for identifying EGFR inhibitors using machine learning approaches
P35 Sidorov Pavel Visualization and analysis of large dataset of chemical reactions using GTM
P36 Afonina Valentina Mapping of the Chemical Universe vs Available Chemical Space of Lead-Like Compounds
P37 Sugimoto Manabu Development and Applications of Electronic-Structure Informatics
P38 Casciuc Iuri Chemical reactions visualization: do outliers make any sense?
P39 Empereur-mot Charly Screening Explorer – An interactive tool for the analysis of screening results
P40 Bräuer Maria Interaction Studies of Bacterial Proteins with Antimicrobial Peptides By NMR

Tutorials of the school

no publication

Tutorial 1

The tutorial requires several software:

  • Chemaxon’s InstantJChem: this is a friendly interface to manage a database on chemical topics. You shall obtain the software through the web page of the editor here. The software can be downloaded and installed for free, but with limited functionality yet sufficient for the present tutorial. Evaluation licenses can be requested for free to the editor, through the contacts web page. For more details refer to the download web page.
  • Weka 3.9.0: a complete open source solution for data mining. It can be downloaded at this page.
  • ExtCrossValidate: an application to split a dataset in SDF format into training and test sets according to various strategies. The software is provided into the USB key of the school. It can be downloaded here:
    • Linux
    • Windows
    • Mac. You need to uncompress the archive to get the application and application bundle.
  • xFragmentor: an application to compute ISIDA Substructural Molecular Fragment descriptors with a GUI interface.
    • Linux
    • Windows
    • Mac. You need to uncompress the archive to get the application and application bundle.
  • xModelAnalyzerR: an application for interactive analysis of regression models compatible with the Weka software outputs.
    • Linux
    • Windows
    • Mac. You need to uncompress the archive to get the application and application bundle.

The dataset is a sample of the IUPHAR database dedicated to the serotonin receptor 5-HT2B (IUPHAR_5HT2B.sdf).

All materials for the tutorial, except the software, are included into this zip archive.

Tutorial instructions are located here.

Tutorial 2

The tutorial requires the use of the KNIME software. It is provided on the USB keys of the school. It can be dowloaded on the download page of the software editor. The software can be downloaded and used for free.

The tutorial uses the PLANTS software for docking. But for reasons of time, all the outputs generated by the software on the test cases are provided. Therefore, it is not necessary to have access the PLANTS software to perform the tutorial.

The tutorial will focus on the analysis of the docking outputs generated by the PLANTS software using KNIME. All files are provided into zip archive.

Instructions can be found here:

Photos of the School


Family Photo

CS3 2016 family photo
Participants to the Chemoinformatics Strasbourg Summer School
R. Nugmanov

High resolution here.