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Strasbourg Summer School - 2010

Chemoinformatics Strasbourg Summer School, Obernai 2010

The Strasbourg Summer School on Chemoinformatics 2010 will take place in Obernai.

This manifestation is organised by:

  • the French Society on Chemoinformatics (SFCi, Société Français de Chemoinformatique)
  • the International Cheminformatics and QSAR Society


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

You can find all informations of the lectures in the Program section of this site.

First Circular

(click to download)

Pre-conference events

Friday 18 June (Faculty of Chemistry, University of Strasbourg)

French - Japanese workshop on computational methods in chemistry

Organizers: A. Varnek, C. Daniel (France) and K. Funatsu (Japan)

Abstract submissions should be send to chemoinfo-school@unistra.fr

Information about Obernai and the VVF "Les Géranium"


  • VVF Canterelle d’Obernai Les Géraniums, Obernai, France.

Situated just 25 km from Strasbourg, at the foot of Mont Sainte Odile, Obernai lies on the famous "route des vins". It is renowned for its breweries, its wood-frame houses, quaint little streets and city ramparts. The perfect starting point to discover the traditions and cuisine of Alsace. The school will be held in the village of vacation "VVF - Les Geraniums" which provides all required facilities.

Group transportation

  • On Sunday 20 June group transportation (two buses) will be arranged from Strasbourg railway station – via Strasbourg-Entzheim airport – to the venue.
  • Bus departure times will be as follows:
    • from Strasbourg railway station: 13.30 and 15.00
    • from Strasbourg airport: 14.00 and 15.30.
  • Bus transportation back to the station and to the airport will also be arranged for Thirsday 24 June afternoon. Departure times will be finalised at a later stage in order to suit the majority.

For further information, please consult the Practical Information Guide PDF version:

Practical informations

Members of the Scientific Board

Scientific Advisory Board

  • Luc Morin-Allory, France
  • Jurgen Bajorath, Germany
  • Edgar Jacoby, Switzerland
  • Kimito Funatsu, Japan
  • Didier Rognan, France
  • Gisbert Schneider, Switzerland
  • Alex Tropsha, USA
  • Alexandre Varnek, France
  • Bruno Villoutreix, France


Sources of Money


This manifestation is supported by:

Centre National de la Recherche Scientifique
Société Française de Chemoinformatique

Schrödinger for Computational Drug Design
Schrödinger provides accurate, reliable, and high performance computational technology to solve real-world problems in life science research
Inte:Ligand GmbH
assists scientists and management in the pharmaceutical, life science, nutrition and cosmetic industries to improve their efficiency in identifying new bio-active molecules. This is achieved by developing and delivering innovative scientific software, novel in silico tools, and expert consulting services that facilitate the decision making process for prioritizing compounds for further experimental assessment.
Sanofi Aventis

Under construction...

Who’s behind the scene

Local Organizers

  • Alexandre Varnek, University of Strasbourg, France
  • Didier Rognan, CNRS, Illkirch, France

e-mail: cheminfo-school@chimie.u-strasbg.fr

Registration Contact

Cellule Congrès

21, rue du Maréchal Lefebvre 67100 Strasbourg, FRANCE

Phone: +33 3 68 85 49 40, Fax: +33 3 68 85 49 41

Program of the School

Scientific Program

The program of the school includes: opening lectures on 20 June, 7 half-day scientific sessions (lectures and tutorials), software presentations and a poster session.

The following main topics are selected for the lectures:

  • Molecular similarity and diversity analysis
  • Molecular descriptors and molecular representations
  • Machine-learning methods in chemistry
  • Obtaining, validation and application of QSAR models
  • Virtual screening
  • In silico pharmacology

The tutorials on 21-23 June will be devoted to some aspects of ligand-based and structure-based virtual screening, and structure-property modeling.

Program of the lectures

20 June
Opening lectures
17:00-18:00 Hugo Kubinyi Chemoinformatics in Drug Discovery - Quo Vadis?
18:00-19:00 Wendy Warr Room for a small one?
19:00 Welcome party
21 June
9:00-10:00 Thierry Langer Pharmacophores: Well Suited Tools For Accurate Virtual Screening
10:00-10:20 Coffee break
10:20-11:20 Igor Tetko, T. Oprea Early ADME/Tox predictions: toy or tool?
11:20-12:20 Didier Rognan Fingerprinting protein cavities and protein-ligand complexes in rational drug design
12:20-14:00 Lunch
14:00-15:30 Denis Fourches Data cleaning
15:30-15:50 Coffee break
Lectures from Software Editors
15:50-16:20 Schrödinger
16:20-16:50 BioSolveIT
16:50-19:00 Poster session
22 June
9:00-10:00 Alexander Tropsha Best practices for chemical data curation and QSAR model development and application for lead discovery
10:00-10:20 Coffee break
10:20-11:20 Jean-Philippe Vert Machine learning methods in chemistry and chemogenomics
11:20-12:20 Edgar Jacoby The role of chemoinformatics in the design of a comprehensive drug discovery screening collection
12:20-14:00 Lunch
14:00-16:00 Igor Baskin, Gilles Marcou Ensemble modeling in QSAR
16:00-16:20 Coffee break
Lectures from Software Editors
16:20-16:50 OpenEye
16:50-17:20 Accelrys
17:20-17:50 Tripos
23 June
9:00-10:00 Gisbert Schneider Computer-assisted drug design: From ligands to pockets and back again
10:00-11:00 Christoph Sotriffer Docking and scoring of protein-ligand complexes: What is possible and what is not?
11:00-11:20 Coffee break
11:20-12:50 Thierry Langer, Sharon Bryant Screening with pharmacophores using LigandScout 3.0
13:00-14:30 Lunch
14:30-16:00 Esther Kellenberger Cross-docking
16:00-16:20 Coffee break
16:20-17:20 Christopher A. Lipinski Chemoinformatics and Medicinal Chemistry: Rules, Filters and Common Sense
19:00 Conference dinner
24 June
9:00-10:00 Johann Gasteiger Modeling Chemical Reactions in Drug Design and Chemical Risk Assessment
10:00-10:20 Coffee break
10:20-11:20 Andreas Bender From Single-Target Models to Multiple-Target Models - Extrapolating in Target Space Using Proteochemometrics Approaches
11:20-12:20 Klaus-Jürgen Schleifer Challenges in Agrochemicals Design
12:20-12:30 Closuring
12:30-14:00 Lunch
14:00 Departure to Strasbourg airport or main station by bus

We are sorry to announce that the lecture of Thomas Engel on
The History of Chemoinformatics is canceled for medical reasons.

How to Register

Registration Contact

Cellule Congrès

21, rue du Maréchal Lefebvre 67100 Strasbourg, FRANCE

Phone: +33 3 68 85 49 40, Fax: +33 3 68 85 49 41

Abstracts submission

Abstracts should be submitted to the Organizers by e-mail as the attachment in RTF or DOC format.

e-mail: chemoinfo-school@unistra.fr

The abstract should be prepared according to the following rules:

  • 1 page, Times New Roman 12 pts, 1.5 spaces between lines, justified, margins: 3 cm, 3 cm, 3 cm, 3 cm;
  • Title: centered Times New Roman 14 pts, Bold;
  • Authors (bold) and address: Times 12 centred

Registration form

Click to download

Registration form

Registration form

Conference Fee






not available










L’école est gratuite pour toute personne rémunérée par le CNRS.

The conference fee covers:

  • Participation in the school,
  • teaching materials,
  • lodging in "VVF Les Geraniums", 4 nights from 20 June to 24 June 2010,
  • welcome reception on 20 June,
  • breakfast and lunch on 21-24 June,
  • coffee breaks,
  • conference dinner on 23 June,
  • shuttle service from the central railway station and from the airport of Strasbourg to "VVF Les Geraniums" on 20 June and on 24 June.

Collection of poster abstracts

Poster abstracts

List of posters to download

List of posters

Click on poster’s title to access the abstract.

Poster ID Authors and Title
P-1 A. J. M. Barbosa, F. Caporuscio, G. Mangiatordi, G. Rastelli, A. Del Rio
CoCoCo: a freely available multiconformational database of commercial compounds for HTVS purposes. Application to the FXR nuclear receptor
P-2 C. D. Fjell, H. Jenssen, W. A. Cheung, R. E. W. Hancock and A. Cherkasov
Cheminformatics Optimization of Antibacterial Peptides using Genetic Algorithm
P-3 F. Chevillard
Beyond measuring the performances of ligand-based methods for back-screening selections
P-4 G.-Yu Chuang, D. Rognan
Hs-Pharm-Gen: An Automated Tool For Generating Receptor-Based Pharmacophores From Ligand-Free Protein Structures
P-5 K. Hasegawa, T. Fukami, M. Ohta, Y. Shiratori
Construction of ADMET local models and development of Web GUI for chemists
P-6 F. Dulin, M. Pierre Halm, A. Lepailleur, R. Bureau, S. Rault
Prediction of pesticides toxicity to bees: database construction and QSAR studies
P-7 N. Dupont, J. Pérard-Viret, E. Migianu-Griffoni, M. Monteil
Ligand based and structure based in-silico optimisation and design of αvβ3 integrin ligands for detection of integrin overexpression in tumor cells by a new MRI nanoplatform
P-8 D. Fourches, E. Muratov, A. Tropsha
Trust, but verify: On the importance of chemical structure curation in cheminformatics and QSAR modeling research
P-9 C. Gaudin, E. Ivanoff G. Maurin, D. Paula de Cuhna, P. Horcajada, C. Serre
Quantitative Structure Activity Relationship of metal-organic frameworks as potential nanocarriers for drug encapsulation and delivery
P-10 C. Coiffier, E. Henon, P. Goekjian A. Haudrechy
Top-down approach for research of new biologically active substrates:
Analysis of preferred conformations of C-pentosides
P-11 J. Desaphy, D. Rognan
Predicting binding site similarity from pharmacophore-annotated cavity shapes
P-12 A. Kooistra, T. W. Binsl, C. de Graaf, J. H. G. M. van Beek, J. Heringa
EDprints: improved virtual screening using assembled information of electron density
P-13 S. R. Langdon, N. Brown, J. Blagg
The scaffold diversity of exemplified medicinal chemistry space
P-14 J. Graton, J.-Y. Le Questel, C. Laurence
The pKBHX Database: Towards a Better Understanding of Hydrogen-Bond Basicity
P-15 A. Lepailleur, S. Lemaître, X. Feng, J. Sopkova-de Oliveira Santos, P. Delagrange, J. Boutin, P. Renard, R. Bureau, S. Rault
Novel 2,2′-Bithienyl Derivatives as Non-Peptidic AANAT inhibitors : a Computational Approach from Hit Discovery to Lead Optimization
P-16 E. Leproult, D. Moras, J.-M. Wurtz
Design of highly selective covalent kinase inhibitors
P-17 Yann Lienhart
Magellan: a database application to store and help the analysis of mass spectrometry and gas chromatography data
P-18 K. Loving, N. Salam, W. S. Schrödinger
Computational Tools For Fragment-Based Drug Discovery
P-19 S. Lozano, M.-P. Halm-Lemeille, A. Lepailleur, R. Bureau, S. Rault
Genetic algorithm and consensus QSAR: application to acute toxicity
in fish
P-20 J. Meslamani, D. Rognan
Predicting Ligand-Protein Binding Using Svm: A Novel Chemogenomic Screening Method
P-21 P. Muller, V. Vivat, D. Roecklin, M. Uhirng, P. Ciapetti, D. Zeyer
HSP90 inhibitors: hit finding using Molecular Interaction Fingerprint and non-covalent ESI-MS screening
P-22 E. N. Muratov, D. Fourches, A. G. Artemenko, V. E. Kuz’min, G. Zhao, A. Golbraikh, P. G. Polischuk, E. V. Varlamova, I. I. Baskin, V. A. Palyulin, N. S. Zefirov, L. Jiazhong, P. Gramatica, T. Martin, F. Hormozdiari, P. Dao, C. Sahinalp, A. Cherkasov, T. Oberg, R. Todeschini, V. Poroikov, A. Zaharov, A. Lagunin, D. Filimonov, A. Varnek, D. Horvath, G. Marcou, C. Muller, L. Xi, H. Liu, X. Yao, K. Hansen, T. Schroeter, K.-R. Muller, I. Tetko, I. Sushko, S. Novotarskyi, J. Reed, J. Barnes, A. Tropsha
Combi-QSAR Modeling of Ames Mutagenicity
P-23 B. Plainchont, J.-M. Nuzillard
V. De Paulo Emerenciano
Recent developments of LSD, an automatic structure elucidation software
P-24 M. Nuzillard, A. Haudrechy
Quiral: a Computer Program for the Synthesis of Chiral Molecules from Sugars
P-25 S.Pérot, C.Reynes, O.Sperandio, M.Miteva, B.Villoutreix, A-C.Camproux
Anatomy of druggable pockets and associated ligands
P-26 V. Ramachandran, G. Hansen, R. Hilgenfeld
Targeting Mip proteins for the development of new antibacterials
P-27 L. Colliandre, A. Ahmed-Belkacem, C. Hurard, C. Roumestand, D.Douguet, W. Bourguet, G. Labesse, J.-M. Pawlotsly, J.-F. Guichou
Implementation and application of a fragment-based screening approach to find news humans cyclophilins inhibitors
P-28 M. P. A. Sanders, J. P. G. Klomp and J. de Vlieg
Sequence based residue selection and the application in drug design
P-29 E. Varlamova , E. Muratov, A. G. Artemenko , V.E. Kuz’min, L. Nikolaeva-Glomb, A. S. Galabov
QSAR modeling of poliovirus replication inhibition by mixtures of antivirals
P-30 P. Vayer, A.Arrault, M. Bertrand
ChemoMining approach of the management of pharmaceutical screening projects
P-31 M. Wirth, W. Sauer, O. Michielin
Do Ligands of different Drug Targets show specific Molecular Shapes?
P-32 G. Wissel, H. Xhaard
Molecular modeling of antagonist binding at the α2 Adrenoceptors
P-33 Y. Yamanishi
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework
P-34 J. Maupetit, B.Villoutreix, P. Tufféry
3D Printing Service @ RPBS - MTi
P-35 N. Chitranshi, S. Gupta, P. K. Trpathi
Computational Studies of Huntingtin protein: Classification and Binding Pattern Determination
P-36 M. Stahl
Exploring Local Shape Space with Fragment Replacement
P-37 C. Muller, G. Marcou, A. Varnek
Predictive models to detect incorrect a tom-atom mapping of reactions using condensed graph of reactions
P-38 A. de Luca, G. Marcou, D. Horvath, A. Varnek
Recognition of different classes of reactions using condensed graphs of reactions
P-39 I. Oprisiu , G. Marcou, A. Varnek, E. Varlamova, E. Muratov, V. Kuzmin
Modeling of phase diagrams
P-40 D. Horvath, C. Chira
Simplified Chain Folding Models as Metaheuristic Benchmark for Tuning
Real Protein Folding Algorithms?
P-41 B. Wendt
Capturing SAR-trends from chemogenomical spaces
P-42 V. Le Guilloux, G. Guenegou, S. Bourg, J. Dubois-Chevalier, L. Morin-Allory, L. Colliandre
Implementation of a Reference “Chemical Space” for HTS Commercial Compounds: Application to the Comparison of Chemicals Libraries.

Tutorials of the school

no publication

Data Cleaning

This tutorial is dedicated to inspection and curation of compound databases.




Softwares: Chemaxon Strandardizer/JChem

Ensemble Learning

This tutorial is dedicated to ensemble learning in chemoinformatics, both in the context of classification and quantitative models.



Softwares: Weka-3-7, ISIDA/ModelAnalyzer


This tutorial is dedicated to docking, focusing on binding site preparation and impact of expert choices on docking and screening success.



Software: FlexX


This tutorial is dedicated to pharmacophore elucidation and design, and to their use in virtual screening.



Softwares: LigandScout


Here are the softwares used during the tutorial. Softwares are provided for direct download when possible, in order to guarantee that school attendees can use the very same versions.

Otherwise, follow the link to the relevant editors websites, register and download the appropriate version for your operating system. Licenses will be provided for the duration of the school. They will be included, along with all materials for the school on an USB memory stick which will be distributed to each participant.

If relevant, softwares are provided for 32bits systems unless stated otherwise.

Computer requirement

All tutorials and softwares can run on computer using 2Go of RAM and AMD4000+ or Intel Celeron E1600 processors or better. Most softwares will work on Microsoft, Linux or Apple systems with the following exceptions:

  • ISIDA/Duplicates runs only on WIndows
  • LeadIT do not run on Apple systems currently






Please, register to ChemAxon web site and download JChem 5.3.3.


ChemAxon provides free academic licences.



Please download LeadIT1.1.1 from the BioSolveIT website. It will also be provided on the USB memory stick distributed to the participants.

Evaluation licences valid until July 12th 2010 will be provided during
the school.

They may be extended up to the end of September 2010 by email
request to license@biosolveit.de.
Please specify that you participated at this school in your mail.

Note: The evaluation licence will cover much more than what will be used in the tutorial, namely:

  • FlexX & the built-in Corina for ring conformers
  • FlexX-Pharm
  • ReCore
  • FTrees
  • FlexS
  • 2Ddraw
  • PoseView

Note: ReCore will not be used in the tutorials. But if you want to use ReCore, you will need to create a so-called ReCore Fragment Index (*.rsx file). A smaller index to get started is shipped with the software:

  • Windows: keep the respective box ticked in the last step of the
  • Linux: go to recore_index/ and run the shell script in there.

Please mind that an index takes roughly 20mins to be created and will consume 700+MB on the hard disk plus similar temporary space during creation.


Inte:Ligand GmbH
assists scientists and management in the pharmaceutical, life science, nutrition and cosmetic industries to improve their efficiency in identifying new bio-active molecules. This is achieved by developing and delivering innovative scientific software, novel in silico tools, and expert consulting services that facilitate the decision making process for prioritizing compounds for further experimental assessment.

Please download LigandScout3.0

The personal license serial number required for using LigandScout 3.0 will be sent to the participants via email.


You can download here the pictures of the event (.zip format) :

Pictures of Obernai
Pictures of the Sessions