EUGM 2008 user presentations

ChemAxon 0815c054e1

23-05-2008 20:29:37

EUGM 2008 Client Presentations

Archive of all Clients' Presentations of UGM 2008 Visegrad

This is the scientific presentation list ordered according to presentation sequence.

If visitors would like to forward questions to authors please send an email to and I can forward to the author.

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ChemAxon 0815c054e1

24-05-2008 20:32:01

Wednesday May 7th

Title: ChemAxon and an Electronic Research Habitat at the Biopolis

Presenter: Peter Condron

Institution: Experiment Research Centre, Singapore

Abstract: The Experimental Therapeutics Centre, the newest A*STAR Research Institute is located at the Biopolis, Singapore’s bio-medical research campus. ETC was formed to “mine the gap” between basic and applied biomedical research, enhancing high potential projects in order to move them towards commercial development. To manage the various high through-put technology platforms that have been assembled at ETC in support of our mission, we have constructed an “Electronic Research Habitat”, a comprehensive hardware and software infrastructure designed to effectively manage terabyte dataflows in the context of ETC’s knowledge based workplace. We implemented ChemAxon as the Habitat's cheminformatics platform and describe here our on-going development and integration of ChemAxon into our electronic environment.

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ChemAxon 0815c054e1

24-05-2008 20:41:27

Title: Evotec Compound Registration System

Presenter: Catherine Reisser

Institution: Evotec

Abstract: Evotec are currently developing a registration system, which will be available on all scientists' desktops. It is relying on Marvin and the JChem cartridge technology.

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ChemAxon 0815c054e1

24-05-2008 20:43:22

Title: ChemAxon's JChem Nodes on the KNIME workbench

Presenter: Shunichi Ozawa

Institution: Infocom Corporation

Abstract: Not only Computer Chemists but also various researchers access a lot of different software and data resources in a broad range area in drug discovery. The workflow solution that can deal with the combination of different applications and data sources as the protocol in the same platform is recognized as very effective tools.

"KNIME" is a workflow solution that ( in Germany develops, and is distributed free of charge as open source. Major modeling software development companies such as SCHORODINGER and Tripos are already partners of KNIME. So it seems that KNIME considers the use of modeler as well as cheminformatician.

This time, Infocom released "JChemExtensions" that is able to use the ChemAxon tool with core capabilities for structure visualization, search

and management, property prediction on the KNIME. It also make use of the characteristics of chemical structure search engine of JChem, so

researchers can access chemical structures stored in a JChem data cartridge or other relational database on the KNIME workbench. We will demonstrate a number of nodes and show how easy it is to make

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ChemAxon 0815c054e1

24-05-2008 20:49:06

Thursday May 8th

Title: Very large databases and 2D- and 3D-Similarity Searching

Presenter: Lutz Weber

Institution: OntoChem

Abstract: Using different hardware platforms / operating systems we have explored different possibilities to build and implement JChem based chemical-biological databases with more than 100 million chemical compounds. These datasets are then subject to various 2D and 3D similarity searching methods to provide ideas for novel molecules of biological interest. We will show examples for using these integrated technologies for lead finding.

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ChemAxon 0815c054e1

24-05-2008 20:51:24

Title: Evotec's Library Profiler tool

Presenter: Alistair Sedwell

Institution: Evotec

Abstract: Evotec have developed a Library Profiler tool based on ChemAxon toolkits to allow scientists to analyse and filter large combinatorial virtual libraries into smaller libraries or compound sets.

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ChemAxon 0815c054e1

24-05-2008 20:52:27

Title:VSEngine - Similarity & Property prediction based Virtual Screening Web Services

Presenter: Dragos Horvath

Institution: CNRS

Abstract: Academic scientists from the chemoinformatics group of Prof. Varnek (Laboratoire d'Infochimie, UMR 7177 - Université Louis Pasteur, Strasbourg) have developed over time various innovative virtual screening applications (novel - fragment & pharmacophore - descriptors, similarity scoring techniques, massively parallel mining for QSAR models, novel applicability domain definitions & linear/nonlinear consensus scoring schemes, condensed graph-based modeling of chemical reactivity, etc). One month ago, our group started an effort to set up a virtual screening web service allowing non expert users to access these techniques on line in order to mine for potentially interesting compounds within the web server's molecule database, ScreenDB. This latter is thought to regroup sets of commercially or academically available compounds, in addition of reference molecules of known properties - from publicly available QSAR training sets, intended to serve as "seeds" (specific alerts will be issued automatically as soon as a query is found to have returned an abnormally high concentration of reported actives against a given target). The challenges faced during the development of these integrated web services are of technical nature - making the various heterogeneous approaches to work with each other and with the classical substructure & similarity search engines. This can be quite naturally achieved with the ChemAxon toolbox, in charge of all the aspects concerning compound standardization & formal charge assignment, MySQL database management, molecular format interconversion, standard (sub)structure & similarity searches, physicochemical property & descriptor calculations, hit visualization, etc.

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ChemAxon 0815c054e1

24-05-2008 20:54:41

Title: IBEX - access and exploit SAR data from patents and journals

Presenter: Peter Varkonyi

Institution: Astra Zeneca R&D, Mölndal

Abstract: IBEX is a global AstraZeneca application to access GVKBio's Medicinal Chemistry and Target Databases containing SAR data extracted from medicinal chemistry journals and patents. At GVKBio expert curators populate these databases with explicit relationships between published documents, compounds, assay results and sequences. A web-based application, IBEX provides an intuitive search interface to query more than 3 million entries representing over 2 million unique structures and 10 million SAR points. It uses ORACLE database technology and JChemBase and Marvin to handle chemical searches and structural visualisation. IBEX is currently used in medicinal chemistry projects for prior art checking, library design, ligand- and structure-based virtual screening. It allows AstraZeneca scientists (medicinal chemists, computational chemists, bioinformaticians) to explore wider relationships between ligands and target families. Examples of patent visualisation using, for example, ChemGPS chemical space and patent series identification using molecular frameworks will be given.

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ChemAxon 0815c054e1

24-05-2008 20:55:52

HSP90 Ligands Chemical Diversity of Known Molecules and Discovery of New Potential Hits by Virtual Screening

Presenter: Davide Audisio

Institution: Aureus Pharma

Abstract: Hsp90 has emerged as a promising target for new cancer therapeutics, with the perspective of simultaneous disruption of a large range of oncogenic pathways. HSP 90 Inhibitors could result in cytostasis or cell death. Diverse inhibitors of this chaperone protein are currently under intensive study due to their potential role in regulating cellular proliferation.

Patented and published structure-activity relationships on HSP90 inhibitors were organized in the Aureus Pharma knowledgedatabase format. The HSP90 dataset contains chemical structures linked to their biological activities as well as the detailed description of the experimental protocols used for biological testing. Chemical diversity analysis were performed using either the molecular descriptors calculated with Calculator Plugins (ChemAxon) and a radar-type visualization or by clustering using JKlustor (ChemAxon). Active molecules were extracted and diverse representative derivatives were selected as query molecules to screen the Zinc database. This virtual screening was performed using ChemAxon pharmacophoric fingerprints to identify new HSP90 inhibitors. Several hits were identified at different similarity thresholds and selected on the basis of their chemical novelty for biological testing. Experimental validation is in progress.

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ChemAxon 0815c054e1

24-05-2008 20:57:12

Title: DockingServer: GUI-based molecular docking on the web using Chemaxon tools

Presenter: Eszter Hazai

Institution: Virtua Drug

Abstract: DockingServer ( is an internet service developed by Virtua Drug Ltd that calculates the site, geometry and energy of small molecules interacting with proteins. It offers an easy and effective way for carrying out docking calculations, evaluating and presenting the results of docking calculations, writing method section for reports and organizes docking data.

DockingServer integrates the different tasks arising during the docking calculations by using third-party softwares for different steps. Molecular docking is based on Autodock software, electronic properties of the ligands are calculated with MOPAC and small molecule preparation and visualization are achieved using ChemAxon softwares.

The role of ChemAxon softwares in the DockingServer can be divided into three groups:

1. cxcalc calculations run in the background in order to i, calculate the protonation state of the ligands at a given pH; ii, to achieve rough geometry optimization of the ligands; iii, to calculate IUPAC names for the ligands;

2. file conversion tasks, like sdf conversion to multiple ligands, mol2 -> mol conversion etc. using molconvert command.

3. visualization and input of the ligands in 2D and 3D, visualization of the binding site-ligand interaction is achieved by using MarvinSketch and MarvinView.

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ChemAxon b124dd5f17

28-05-2008 09:52:07

Title: Aureus Pharma lightning round presentation

Presenter: Ismail Ijjaali

Institution: Aureus Pharma

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ChemAxon b124dd5f17

28-05-2008 09:56:22

Title: Reconfigurable accelerator for ChemAxon fingerprint based calculations

Presenter: Attila Berces

Institution: Chemistry Logic

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ChemAxon b124dd5f17

28-05-2008 09:56:38

Title: An integrated suite of applications using ChemAxon components

Presenter: Michael Dippolito

Institution: DeltaSoft

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