Strasbourg Summer School in Chemoinformatics - 2014

General informations

Home

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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

Organizers:

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

Confirmed speakers:

J. Bajorath (University of Bonn, Germany),
I. Baskin (Lomonosov University of Moscow, Russia),
N. Brown (Institute of Cancer Research, London, UK),
G. Cruciani (Università degli Studi di Perugia, Italy),
A. Cherkasov (Vancouver Prostate Center, Vancouver, Canada),
R. Glen (University of Cambridge, UK),
J. Overrington (EMBL-EBI, Cambridge, UK),
M. Rarey (University of Hamburg, Germany),
G. Schneider (ETH, Zürich, Switzerland),
C. Sotriffer (University of Wuerzburg, Germany),
A. Tropsha (University of North Carolina at Chapel Hill, USA),
W. Warr (Wendy Warr & Associates, UK),
P. Willett (University of Sheffield, UK),
B. Villoutreix (University Paris-Diderot, France),
G. Wolber (Free University of Berlin, Germany),
J. Gasteiger (University of Erlangen, Germany),
and J.-M. Lehn (University of Strasbourg, 1987 Nobel Laureate in Chemistry)

Tiny URL of this page: http://tiny.cc/CS3-2014
QR code:

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Pre-conference events

Monday 23rd June 2014 (University of Strasbourg): Crash course in Chemoinformatics (lectures and tutorials).

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Post-conference event

Monday 30th of June and Tuesday 1st of July 2014 (University of Strasbourg): 5th French-Japanese workshop on computational methods in chemistry

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

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Link to lanyrd social conference directory: http://lanyrd.com/2014/csss2014/

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Informations about Strasbourg University

Location

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Strasbourg Summer School - Strasbourg, France, 23-27 June 2014

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).

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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 :

1 : Tour de Chimie (Chemistry Tower)
2 : CDE (European College)
3 : Restaurant "le 32"

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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).

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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.

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Photos by Jonathan Martz and Geneviève Engel.

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Poster abstracts and PDF

Posters and abstracts

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Strasbourg Summer School - Strasbourg, France, 23-27 June 2014

ID	Speaker	Title
P1	Alexandre Borrel	Druggability prediction performances related to different pocket estimations
P2	Cheima Snani	Prediction of retention indices polycyclic aromatic hydrocarbons in gas chromatography
P3	Gennadiy Poda	In Silico Design of Inhibitors as Potential Therapeutics for Multiple Myeloma and Leukemias
P4	Ivan Čmelo	Chemical space mining for new glucocorticoid receptor agonists
P5	Gilles Marcou	Predicting reaction conditions for Michael reactions
P6	Mahendra Awale	Perception of 3D-Molecular Shape and Pharmacophores from 2D-Structures Using Atom Pair Fingerprints
P7	Ayana Dagan-Wiener	Getting better at predicting bitter
P8	Ricardo Visini	Investigation of the structure of LecA and multivalent ligands with crystallography and MD simulation
P9	Tomáš Raček	NEEMP – Tool for parameterization of empirical charge calculation method EEM
P10	Vigneshwari Subramanian	Visually interpretable models of kinase selectivity related features derived from field-based proteochemometrics
P11	Francois Berenger	A rotation-translation invariant molecular descriptor and its use in ligand-based virtual screening
P12	Abraham Yosipof	Data Mining and Machine Learning Tools for Combinatorial Material Science of All-Oxide Photovoltaic Cells
P13	Ainoleena Turku	Screening for small molecule ligands to a peptide binding GPCR
P14	Maykel Cruz-Monteagudo	Probing the Hypothesis of SAR Continuity Restoration by Activity Cliffs Removal in QSAR Modeling
P15	Maykel Cruz-Monteagudo	Toward the computer-aided discovery of FabH inhibitors. Do predictive QSAR models ensure high quality virtual screening performance?
P16	Carla Jamous Delépée	Nonpeptide ligands of Arginine Vasopressin receptor (V2R) : Docking study and conformational analysis
P17	Houari Soltani	Piperazine: Synthesis and molecular modeling
P18	Hakem Atmane	Molecular Modeling Study of Diazinon and its adsorption On Montmorillonite
P19	Franck Da Silva	PPIome – 3D mapping of protein-protein interfaces: Druggable cavity detection and ligand design
P20	Mélaine A. Kuenemann	An exploration of the 3D chemical space has highlighted a shape profile for the compounds intended to orthosterically inhibit protein-protein interactions.
P21	Alban Lepailleur	Peptide and non-peptide ligands of the Urotensin Receptor. Conformational analysis and definition of pharmacophores.
P22	Giuseppe Felice Mangiatordi	A new gating site in Human Aquaporin-4: insights from Molecular Dynamics simulations
P23	Miriam Mathea	Comparison of Different Measures for the Domain of Applicability of Classification Models
P24	Joshua Meyers	Investigating the Conformational Diversity of Endogenous Ligands
P25	Matthieu Montes	Udock, the Interactive Docking Entertainment System
P26	Nathalie Lagarde	NRLiSt BDB : the manually curated Nuclear Receptors Ligands and Structures Benchmarking Database
P27	Nicolas Bosc	Broad profiling prediction of protein kinase inhibitors via Kinochemometrics approach
P28	Petr Čech	Automatic workflow for the classification of local DNA conformations
P29	Priyanka Banerjee	ProTox: A web server for the in silico prediction of rodent oral toxicity
P30	Regina Politi	Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure based modeling methods
P31	Leona Šerá	Pump-Probe Molecular Dynamics Simulations of Allosteric Proteins in GROMACS
P32	Annkathrin Weißenborn	A Novel Approach to Quantify Data Set Topology
P33	Anne Tromelin	In silico study of correspondences between odors descriptions linked to common features of aromas compounds
P34	Kely M.Turra	4D-QSAR of a set of novel β-N-biaryl ether sulfonamide-based hydroxamates for MMP9-inhibition
P35	Milan Voršilák	Scaffold analysis of environmental and drug discovery databases
P36	Xian Jin	Peptide Database Analysis via 3D Shape Fingerprint
P37	Birgit Viira	Structure motifs in HIV1 RT ligand data published in the literature
P38	Geoffrey Gabel	Beware of machine-learning based scoring functions – On the danger of developing black boxes.
P39	Stéphane Azoulay	Rational design of ligands targeting GPCR heterodimers – application to V1B CRHR1 dimer in the treatment of stress, anxiety and depression
P40	Jérémy Desaphy	IChem : A toolkit for Fingerprinting cavities and protein-ligand complexes
P41	Guillaume Poezevara	Automatic Discovery of Molecular Graph Patterns Inhibiting Multiple Drug Transporters
P42	Esther Kellenberger	sc-PDB: a 3D-database of druggable binding sites
P43	Esther Kellenberger	Similarity between biosynthetic enzymes and druggable proteins captured by 3D-computing approach
P44	Dragos Horvath	S4MPLE – Sampler For Multiple Protein-Ligand Entities: Simultaneous docking of several entities.
P45	Dragos Horvath	Computational chemogenomics - is it more than inductive transfer?
P46	Pavel Davidovich	New IL-36 cytokine receptor inhibitors
P47	Giovanni Cincilla	Validation of Pythia’s target prediction
P48	Siti Zuraidah	Mohamad-Zobir Global Mapping of Traditional Chinese Medicine (TCM) Into Bioactivity Space Improves Mechanistic Understanding and Discovers Relationships Between Medicinal Classes
P49	Gunther Stahl	Protein active site comparison with SiteHopper: phylogeny to polypharmacology
P50	José-Manuel Gally	Development of an universal workflow for the preparation of molecular databases for Virtual Screening
P51	Héléna Gaspar	GTM Applicability Domain for Classification and Regression models
P52	Philipp-Maximilian Jacob	Synthesis Route Optimisation Using The Network Of Organic Chemistry

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Program of the School

Program

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Strasbourg Summer School - Strasbourg, France, 23-27 June 2014

Monday 23 June

9:00 - 17:00		Preconference session “Introduction into Chemoinformatics”	Materials
18:00 - 18:10		Opening
18:10 - 19:10	G. Schneider (ETH, Zürich, Switzerland)	Opening lecture: Generating bioactive molecules de novo	abstract	slides
19:15 - 21:00	Welcome Party

Tuesday 24 June

9:00 - 9:40	J. Gasteiger (University of Erlangen, Germany)	Solved and unsolved problems in Chemoinformatics	abstract	slides
9:40-10:20	P. Willett (University of Sheffield, UK)	The calculation of molecular similarity: principles and practice	abstract	slides
10:20-10:40	coffee break
10:40-11:20	J. Bajorath (University of Bonn, Germany)	Exploring activity cliffs from a chemoinformatics perspective	abstract	slides
11:20-12:00	R. Glen (University of Cambridge, UK)	Metabolism: Investigating and predicting how biology changes molecules and their properties	abstract	slides
12:00-14:00	Lunch
14:00-14:20	Gunter Stahl (OpenEye)	Ligand-based Virtual Screening using shape and chemical features	abstract	slides
14:20-14:40	Marcus Gastreich (BioSolveIT GmbH)	Real-Time & Entropy-Aware Lead Optimization	abstract	slides
14:40-15:00	David Rinaldo (Schrödinger GmbH)	[Boosting virtual screening enrichments using data fusion: Coalescing 2D fingerprints, shape, and docking	abstract	slides
15:00-17:00	A. Hart, A. Kos	Tutorial 1 - Data Selection and Treatment with KNIME
17:00 - 19:00	Poster session	Beer & Bretzel

Wednesday 25 June

9:00 - 9:40	J. Overington (EMBL-EBI, Cambridge, UK)	[ChEMBL and SureChEMBL - Open Resources for Chemoinformatics and Drug Discovery	abstract	slides
9:40-12:00	A. Tropsha (University of North Carolina, USA)	[The use of biological descriptors of chemical compounds to enrich traditional chemoinformatics applications	abstract	slides
10:20-10:40	coffee break
10:40-11:20	G. Cruciani (Università degli Studi di Perugia, Italy)	BioGPS: the music of chemo and bio informatics valzer	abstract	slides
11:20-12:00	M. Rarey (University of Hamburg, Germany)	Protein Structures: Closing the Gap from PDB to Modeling Input	abstract	slides
12:00-14:00	Lunch
14:00-14:20	Alexandre Borrel (Univ. Helsinki, Finland)	Druggability prediction performances related to different pocket estimations
14:20-14:40	Matthieu Montes (CNAM, France)	Udock, the Interactive Docking Entertainment System
14:40-15:00	Milan Voršilák (Inst. Chem. Tech., Czech Republic)	Scaffold analysis of environmental and drug discovery databases
15:00-17:00	G. Marcou, D. Horvath	Tutorial 2 - QSAR modeling of compounds profiling
18:30-20:00	Assemblé Générale de Société Française de Chemoinformatique

Thursday 26 June

9:00 - 9:40	N. Brown (Institute of Cancer Research, London, UK)	Bioisosteres and Scaffold Hopping in Medicinal Chemistry	abstract	slides
9:40-10:20	A. Cherkasov (Vancouver Prostate Centre, Vancouver, Canada)	[Targeting protein interaction sites on network-hub proteins as an effective strategy to combat drug resistance	abstract	slides
10:20-10:40	coffee break
10:40-11:20	C. Sotriffer (University of Wuerzburg, Germany)	Empirical scoring functions for docking and virtual screening: Fundamentals, challenges and trends	abstract	slides
11:20-12:00	Gerhard Wolber (Free Univ. Berlin, Germany)	3D Pharmacophore Perception and Screening Algorithms: Challenges and Pitfalls	abstract	slides
12:00-14:00	Lunch
14:00-16:00	E. Kellenberger	Tutorial 3 - Compounds profiling: shape analysis of binding sites and pharmacophore modeling
16:00 - 19:00	Cultural Program
19:00	Conference Dinner

Friday 27 June

9:00 - 9:40	B. Villoutreix (University Paris-Diderot, France)	[Small molecule protein-protein interaction modulators: challenges and opportunities for drug discovery	abstract	slides
9:40-10:20	Igor Baskin (Lomonosov University of Moscow)	[Machine-learning method in property predictions: Quo Vadis ?	abstract	slides
10:20-10:40	coffee break
10:40-11:20	W. Warr (Wendy Warr & Associates, UK)	[Chemical reactions: databases, computer-aided synthesis design, and reaction prediction	abstract	slides
11:20-12:00	J.-M. Lehn (University of Strasbourg, 1987 Nobel Laureate in Chemistry)	Perspectives in Chemistry: From Supramolecular Chemistry towards Adaptative Chemistry	abstract	slides
12:00	Closure

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How to register

Register

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Strasbourg Summer School - Strasbourg, France, 23-27 June 2014

You will find here all useful information to register for the 4th Strasbourg Summer School on Chemoinformatics.

• Abstracts Submission
• Conference Fee
• Registration Form and Contact

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Abstracts submission

Strasbourg Summer School - Strasbourg, France, 23-27 June 2014

Abstracts should be submitted to the Organizers by e-mail before April 15th 2014.
The attachment should be in RTF or DOC format.

e-mail: chemoinfo-school@unistra.fr

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

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

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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.

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Registration form and contact

Online registration

Registration is closed.

Contacts

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

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Conference Fee

Strasbourg Summer School - Strasbourg, France, 25-29 June 2012

• Early registration (before April 15th 2014) :

Industrial	850 €
Academics	550 €
Students	350 €
Accompagnying person	200 €

• After April 15th 2014 :

Industrial	900 €
Academics	600 €
Students	400 €
Accompagnying person	250 €

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Financial and technical supports

Sponsors

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4th Chemoinformatics Strasbourg Summer School - Strasbourg, France, 23-27 June 2014

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Tutorials of the school

no publication

Tutorial 1 - Data Selection and Treatment with KNIME

In order to facilitate a smooth KNIME Workshop experience, please follow the instructions below:

1. Go to KNIME web site and download the special distribution of KNIME provided for this workshop here. This special package provides the latest version of the KNIME Analytics Platform with all required extensions pre-installed. Additionally, it already contains the KNIME Workflows and data files that we will use in the workshop. The file is large (>1gb) so please do this well before the workshop begins.
2. Unpack the archive file (.zip, .dmg, or .tar.gz) to a local directory on your computer.
3. Feel free to post any questions you may have prior to the workshop in the linked forum
   thread.
4. If you want to learn more about KNIME before the workshop, consider having a look at the KNIME youtube channel for guides to getting started and many other topics.

Details of the tutorial are available in the following document:

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Tutorial 2 - QSAR modeling of compounds profiling

The tutorial presents some data mining approaches suited to QSAR approach of profiling problem.

It is based on the MATLAB system and the MALSAR library.

The MathWorks company provided us with a trial version of their software. To get the trial MATLAB software use the login informations provided to you by eMail on Tuesday 17th of June and follow the instructions in this file. Note that you’ll need to create an account on the MathWorks web site.

The MALSAR is free, you can download it anytime.

Materials

The dataset, scripts and precomputed results that will be needed for the tutorial can be downloaded here:

After unpacking this archive you will find 4 folders:
– Exercises: the MATLAB scripts of each exercise.
– Precomputed: matlab data files (.mat) containing precomputed results to avoid lengthy calculations during the tutorial. Of cours, one can prevent the exercises to load these pre-computed results and reproduce them from scratch.
– Scripts: useful MATLAB scripts to factorise command lines for common tasks.
– Datasets: Molecule and descriptor files used in the tutorials. From this material, one can reproduce the tutorial using a different set of molecular descriptors.

Instructions

Detailed instructions for the tutorial are available here.

The slides of the Tutorial are available here.

Write to Gilles MARCOU for any comments on the material or if you noticed errors in it.

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Tutorial 3 - Compounds profiling : shape analysis of binding sites and pharmacophore modeling

This tutorial will be held the 3 computer classes of the Faculty of Chemistry (4, rue B. Pascal, 4th floor) which is next building to CDE. The software is installed on computers in these classes, no licenses will be provided.

It works on Linux and uses command lines. The software presented are based on the C++ OEToolKit from OpenEye.

Detailed instructions are available here:

Slides of the tutorial are available here.

The dataset is available here.

The software are available here.

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Where to find accomodation during the conference

Accomodation

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Strasbourg Summer School - Strasbourg, France, 23-27 June 2014

Accomodation - Nearby hotels

Hotel Esplanade Strasbourg ✯✯
1,boulevard Leblois
67000 STRASBOURG

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
67000 STRASBOURG

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

Room rates from 53 to 91€
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
67000 STRASBOURG

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
67000 STRASBOURG

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

Room rates from 68 to 133€
Breakfast : 9,50€

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

Hôtel des Arts ✯✯
10, place du Marché aux cochons de Lait
67000 STRASBOURG

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

Room rates from 68 to 80€
Breakfast : 6,50€

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

Hôtel Gutenberg ✯✯
31, rue des serruriers
67000 STRASBOURG

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
67000 STRASBOURG

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 Diana Dauphine ✯✯✯
30 Rue de la 1ère Armée
67000 STRASBOURG

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

Room rates from 69 to 195€
Breakfast : 11€

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

Hôtel Beaucour ✯✯✯
5, rue des Bouchers / 5, rue des Boeufs
67000 STRASBOURG

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

Room rates from 78 to 205€
Breakfast : 13,50€

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

Hôtel des Princes ✯✯✯
33, rue Geiler
67000 STRASBOURG

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
67000 STRASBOURG

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

Room rates from 75 to 155€
Breakfast : 13€

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

Hôtel Cour du Corbeau ✯✯✯✯
6-8 rue des Couples
67000 STRASBOURG

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

Room rates starting from 135€
Breakfast : 13,50€

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

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