Java Solutions for Cheminformatics

June 2007

Company and product overview

ChemAxon fingerprintCompany

• Founded in 1998, based in Budapest, Hungary

• Representation in the US, UK and Japan / recently established representation in India and Switzerland

• Wide industry expertise >200 corporate clients + >900 academic users

• Wide cheminformatics expertise (>35 staff) 11 PhD, 20 MSc

Products

• Cheminformatics tools - structure drawing/ editing/ search, transformation, library profiling and property prediction

• Enterprise chemistry database and cartridge technology

• Client driven product design research and development

• Solutions and desktop applications for: drug discovery, biotechnology agrochemistry, scientific publishing, education & life science research

ChemAxon staff

Ferenc Csizmadia - CEO

Business teamAlex Allardyce - Marketing Manager, US sales East

Douglas Drake - US sales West

David Hatch - US sales

Nora Lapusnyik – Marketing

David Spender - European sales

Gyorgy Szondi - Sales Director

Project Management

Gyorgy Pirok - Chief Technology OfficerReactor, Standardizer, Chemical Terms

Miklos Vargyas - Chief Scientific OfficerLibraryMCS, JKlustor, Screen, Fragmenter

Szabolcs Csepregi - Director of Search TechnologiesStructure search, JChem Base & Cartridge, MarkushProject

Akos Papp – Head of Chemical Registration Project

Product Development

Calculator Plugins

Zsolt Mohacsi,Nora Mate

IUPAC Naming: Daniel Bonniot, Rita Vereb

Automatic 3D Molecular StructureGeneration: Odon Farkas, Imre Gabor, Adrian Kalaszi, Imre Jakli, Attila Szabo, Laszlo Antal

Protonation, Partitioning, Charge, Isomers: Jozsef Szegezdi

Marvin

Ferenc Csizmadia Peter Csizmadia Andras VolfordTamas VertseErika BiroJudit Vasko-SzedlarSzilveszter JuhosTamas Somogyvari Peter Vadasz

Product Development

JChem BaseSzabolcs Csepregi, Szilard Dorant, Edvard Buki, Tamas Csizmazia

JChem Cartridge for Oracle Peter Kovacs

Instant JChemTim Dudgeon, Petr Hamernik

Reactor, Standardizer, Metabolizer Gyorgy PirokGUI : Istvan Cseh, Attila Szabo Engine: Zsolt Mohacsi, Nora MateLibraries: Jeno Varga, Erzsebet Czinege, Gyorgy T. Balogh, Eszter Papp, Virag Sagi Kiss

JKlustor, Screen, FragmenterMiklos Vargyas

LibMCSMiklos Vargyas, Judit Vasko-Szedlar

Products Overview

Selected Application Areas

Global licenses

Value added constructions

Websites/portal front and back end

Content/ Educational

Consultancy / development

Product development philosophy

Sophisticated technology

High performance (speed, accuracy, features)

Rounded, industry relevant functionality

Customizable

Extendable

Long term relevance

>1100 active clients

Client driven development

Fast and reliable support

Comprehensive API

Platform independence (Java, .NET)

Marvin Development History

1998

Applets, Molfiles, stereo support, Windows, Unix

SMILES, SMARTS, PDB, Rgroups, isotopes, shortcuts, Marvin Beans

Ball and stickJPG, PNG, SVG, Cut&Paste with Isis/ChemDraw, 2D cleaning, (de)aromatization, reaction drawing

20001999

SDF, RDF, XYZ animations, CML, templates, compressed formats, Swing, 3D models

2001

Mac support, signed applets, Java Web Start, atom mapping

Partial charge,

pKa, logP/logD,

3D optimization, radicals,abbreviated groups

Marvin file format, enhanced stereo, shapes, text boxes, multiple groups, link nodes, TPSA, recursive SMARTS, Donor/Acceptor, electron arrows,

20042003 2005

Tautomers, resonance, lone pairs, conformers, 3D sketching, MarvinSpace,

Topology analysis, presentation quality graphics,...

MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt

MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt

2006

More Plugins,more R-groups,EMF, PDF and Mol2,Improved property storage in MRV, SDfiles and Rdfiles..NET support in MarvinBeans.

2002

2007

Structure to name, Coordinative compounds, Polymer drawing, OLE, Markush enumeration plugin, Multistep reactions

Marvin Survey

JChem Development History

2000

Oracle, MySQL, SQLServer, Access, hashed fingerprints, substructure and similarity search

DB2, PostgreSQL, Rgroup searching

Reaction searching, fragmentation, reaction processing, standardization, pharmacophores, screening

20022001

Clustering, diversity

2003

Cartridge, enhanced stereo searching, recursive SMARTS, Chemical Terms, virtual synthesis

R-decomposition,R-enumeration, reaction library, custom fingerprints, random synthesis, link nodes…

2004 2005

JChem Base http://www.chemaxon.com/JChem_Base.ppt

JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt

2006

Tautomer search, Instant JChem Markush database, reaction similarity, Library MCS, GUI for Standardizer/ Reactor …

2007

Calculated columns, Installer,Tautomer Duplicate filtering, Query tables,

Speed enhancements for

JChem Cartridge form design, relational data for Instant JChem

• New features for Instant JChem, like relational database handling and form design

• Markush structure handling in JChem Base / Cartridge / Marvin

• Markush enumeration Plugin

• Name to structure conversion

• Solubility Calculator Plugin

• Metabolite and Metabolic Stability Prediction

• Toxicity Prediction

• Human CP450 biotransformation library

• Multistep reactions in Marvin and JChem

• Virtual Synthesis Module for Instant JChem

• Application for compound registration system

• QSAR based on 3D conformers

Visit other technical presentations

MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt

MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt

Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppt

Structural Search http://www.chemaxon.com/Structural_Search.ppt

JChem Base http://www.chemaxon.com/JChem_Base.ppt

Instant JChem http://www.chemaxon.com/conf/Instant_JChem.ppt

JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt

Standardizer http://www.chemaxon.com/Standardizer.ppt

Screen http://www.chemaxon.com/Screen.ppt

JKlustor http://www.chemaxon.com/JKlustor.ppt

Fragmenter http://www.chemaxon.com/Fragmenter.ppt

Reactor http://www.chemaxon.com/Reactor.ppt

Find out more

• Product descriptions & linkswww.chemaxon.com/products.html

• Forumwww.chemaxon.com/forum

• Presentations and posterswww.chemaxon.com/conf

• Downloadwww.jchem.com/licensefrset.html