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Strasbourg Summer School on Chemoinformatics: CheminfoS3

VVF Obernai, France, 22-25 June 2008.

The Strasbourg Summer School on Chemoinformatics 2008 took place in Obernai.

This manifestation was organised by:

  • the French Society on Chemoinformatics (SFCi, Société Français de Chemoinformatique)
  • the German Society on Chemoinformatics
  • the International Cheminformatics and QSAR Society
  • Several studentships have been offered by the French Society on Chemoinformatics (Contact organizers)
  • Alexandre VARNEK -Louis Pasteur University (ULP), Strasbourg, France-
  • Didier ROGNAN -National Center for Scientific Research (CNRS), Illkirch, France-

You can find all videos and slides of the lectures in the Program section of this site.

First Circular (click to download pdf version)

Thanks to all the participants!


Scientific program

The program of the school included 5 half-day scientific sessions (lectures and tutorials), presentation of software, a poster session and Round Table discussions.

The following main topics were selected:

  • 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

In the following program, it is possible to access to the slides and videos of the lectures, and to the abstract of the posters presented by the participants to the school.


PDF version

Sunday, 22 June

14:00-17:00 Registration
17:00-17:10 Opening Remarks A. Varnek, D. Rognan
17:10-17:40 QSAR: discovery and first steps T. Fujita film-reel icon
17:40-18:20 History and challenges of chemoinformatics J. Gasteiger film-reel icon
18:20-19:00 Current trends in cheminformatics W. Warr film-reel icon
19:00 Welcome party

Monday, 23 June (morning session) Molecular Similarity Analysis in Virtual Screening

8:30-09:30 Fingerprint Design and Molecular Complexity Effects J. Bajorath film-reel icon
9:30-10:30 Diversity Analysis and Library Design V. Gillet film-reel icon
10:30-10:45 Coffee break
10:45-11:45 De novo Design G. Schneider film-reel icon

Monday, 23 June (after-noon session)

14:00-15:00 Lessons learned from modelling bioactivity - what works and what doesn’t R. Glen film-reel icon
15:00-16:00 How many drug targets? and other questions... T. Oprea film-reel icon
16:00-16:15 Coffee break
16:15-17:30 Tutorial: Impact of dataset composition on models performance N. Weill, G. Marcou, D. Horvath, A. Varnek and D. Rognan
17:45-19:00 Meeting SFCi (Albert Schweitzer hall)
17:45-19:00 Software demonstration (Hansi hall)

Tuesday, 24 June (morning session) QSAR/QSPR strategies, ADME/Tox predictions

8:30-09:30 Molecular descriptors: an overview R. Todeschini film-reel icon
9:30-10:30 The good, the bad and the ugly practices of QSAR modelling A. Tropsha film-reel icon
10:30-10:45 Coffee break
10:45-11:45 Pharmacophore Approach in Drug Discovery T. Langer film-reel icon

Tuesday, 24 June (after-noon session)

14:00-15:00 Classification of chemical resactions J. Aires-de-Sousa film-reel icon
15:00-16:00 Modern Machine Learning Regression Methods I. Tetko, I. Baskin
16:00-17:00 Tutorial 2a. Benchmarking of Different Machine Learning Regression Methods

Tutorial 2b. Descriptor Selection Bias.

I. Baskin, I. Tetko and A. Varnek
17:00-17:15 Coffee break
17:00-18:00 Poster session (Bertoldi hall)

Wednesday, 25 June (morning session) Bio- and Chemoinformatics: Key Technologies within the Drug Discovery Process

8:30-9:15 In silico target profiling J. Mestres film-reel icon
9:15-10:15 Docking and post-docking strategies D. Rognan film-reel icon
10:15-10:30 Coffee break
10:30-11:15 What Crystal Structure Databases Tell us about Conformational Preferences of Drug-like Molecules M. Stahl film-reel icon
11:15-12:00 The Role of Cheminformatics in the Modern Drug Discovery Process P. Ertl film-reel icon

Wednesday, 25 June (after-noon session)

14:00-16:00 Round Table A. Tropsha, P. Vayer, L. Morin-Allory Hot topics in chemoinformatics

Teaching chemoinformatics

16:00 Closing Remarks A. Varnek, D. Rognan


The SFCi / SANOFI-AVENTIS prize for the most innovative poster awarded to poster 12: Graph representation of molecular datasets: applications to dataset visualization and comparison using graph indices, Denis Fourches and Alexander Tropsha.

ID Title Authors
1 "Grider", a visual data mining tool for inspection of chemical spaces. Extension to diversity exploration. Alban Arrault, Véronique Hamon, Philippe Vayer, Marc Bertrand
2 New guided docking approaches for virtual screening and drug design M. Bhattacharyya, J. Seco, F. J. Luque, X. Barril
3 Statistical Approach of Structure-Activity Relationships: A Case Study Sorana D. Bolboacă, Lorentz Jäntschi
4 Ligand Unbinding from the Estrogen Receptor; A theoretical study of molecular mechanics and specificity Sofia Burendahl, Lennart Nilsson
5 A computational chemistry application of the Kepler scientific workflow platform J. M. Campanera Alsina, X. Barril, F. J. Luque
6 SAMFA: how much can we simplify molecular description without sacrificing predictive ability of 3D-QSAR models? John Manchester, Ryszard Czerminski
7 Selective virtual screening for partial and full agonists in the beta2 adrenergic receptor crystal structure Chris de Graaf, Didier Rognan
8 Embedded Molecular Geometry and Molecular Topology Approach for Structure - Activity Relationships Lorentz Jäntschi, Sorana D. Bolboacă
9 Chemoinformatics module for CMKb, a Customary Medicinal Database Varun Khanna, Jitendra Gaikwad , Joanne Jamie , Shoba Ranganathan
10 An integrated methodology to interface structure- and ligand-based drug design Ilenia Giangreco, Orazio Nicolotti, Teresa Fabiola Miscioscia, Paola Tedeschi,Andrea Carotti, Francesco Leonetti, Angelo Carotti
11 An Artificial Neural Network Approach to Pre-screening of Large Chemical Datasets Gohar Margaryan, Rick Stevens
12 Graph representation of molecular datasets: applications to dataset visualization and comparison using graph indices. Denis Fourches and Alexander Tropsha
13 Design of high affinity inhibitors of DNA polymerase beta by virtual screening and NMR Corinne Hazan
14 Comparative Structural and Energetic Analysis of Receptor-Ligand Interactions S. Henrich, S. Richter, T. Wang, R. R. Gabdoulline, R. C. Wade
15 Multicomponent QSPR in Estimation of Rate of Nucleophilic Substitution at Saturated Carbon Karpov P.V., Kravtsov A.A., Baskin I.I., Palyulin V.A., Zefirov N.S.
16 Similarity for reaction using the concept of Condensed Graph of Reaction. F. Hoonakker, A. Varnek
17 Data Integration and Knowledge transfer: Application to the tissue:air partition coefficients Cédric Gaudin, Gilles Marcou, Philippe Vayer, Igor Baskin, Anil Kumar Pandey, Igor Tetko, Alexandre Varnek
18 Ensemble approach to applicability domains of SAR/QSAR models. N. Kireeva, G. Marcou, A. Varnek, I. Baskin, K. Migita, M. Arakawa, K. Funatsu
19 COMET - Predictive Tool to Assess Stability of Metal Complexes in Solution. N. Kireeva, G. Marcou, V.P. Solov’ev, D. Fourches, O.Klimchuk and A.Varnek
20 Application of Molecular-Similarity Networks for Chemoinformatics Research Zsolt Lepp, Chunfei Huang, Takashi Okada
21 Different Handling of a Hydrophobic Pocket and Consequences for Screening Results in Catalyst, Phase and MOE Gudrun M. Spitzer, Martina Mangold, Theodora M. Steindl, Hannes G. Wallnoefer, Christian Laggner, Thierry Langer, Klaus R. Liedl
22 MMsINC®: a new public large-scale chemoinformatics database system J.Masciocchi, M.Fanton, M. Floris, G. Frau1, M. Sturlese, P. Palla1, F. Cedrati, S.Moro, P. Rodriguez-Tomé
23 Integration Framework to Build Powerful Applications for Pharmaceutical Research Aurélien Monge
24 HiT QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis Eugene N. Muratov, Kun Wang, Alexander Golbraikh, Victor E. Kuz’min, Anatoly G. Artemenko, Leonid Gorb, Mohammad Quasim, Jerzy Leszczynski, Alexander Tropsha
25 Expanding the small-molecule GDB with focused libraries of ligands for glutamate receptors Kong Thong Nguyen, Jean-Louis Reymond
26 GemsBond : an algorithm for discovering synthesizable bonds in molecular graphs. Application to the retrosynthetic analysis Frédéric Pennerath, Philippe Jauffret, Claude Laurenço, Gilles Niel, Philippe Vismara and Amedeo Napoli
27 SiteAlign: a simple and fuzzy method to measure similarity between binding sites C. Schalon, J.-S. Surgand, E. Kellenberger, D. Rognan
28 Glide XP fragment docking and structure-based pharmacophores Sherman W., Friesner R.
29 Analysis of DNA Minor Groove Binding Patterns Gudrun M. Spitzer, Bernd Wellenzohn, Patrick Markt, Johannes Kirchmair, Thierry Langer, Klaus R. Liedl
30 Development of Multi Component Molecular Theory and its Application Masanori Tachikawa
31 Determination of 2D pharmacophore with a new algorithm for determining emerging patterns. Application to 5-HT7 ligands. Thibault Varin, François Rioult, Ronan Bureau, Sylvain Rault
32 Monoamine ligands binding to the dopamine, norepinephrine and serotonin transporters : through ionic interactions or sodium chelation ? Henri Xhaard, Mark S. Johnson
33 The Novartis Kinase Compendium : Overview and Applications Eric Vangrevelinghe, Nikolaus Stiefl, Greg Landrum and Pascal Furet
34 Development of new in silico methods to identify ligands for orphan GPCRs. N. Weill, D. Rognan
35 Discovery of potent and selective inhibitors of serine acetyltransferase, an enzyme unique to Entamoeba histolytica Subhash M. Agarwal, Alok Bhattacharya, Amir Azam
36 Conformational sampling and Docking by a GRID-deployed genetic algorithm Alexandru-Adrian Tantar, Sébastien Conilleau, Benjamin Parent, Nouredine Melab, Lorraine Brillet, Sylvaine Roy, El-Ghazali Talbi and Dragos Horvath