Java Solutions for Cheminformatics June 2007 Company and product overview

ChemAxon fingerprint Company 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 team Alex 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 Officer Reactor, Standardizer, Chemical Terms Miklos Vargyas - Chief Scientific Officer LibraryMCS, JKlustor, Screen, Fragmenter Szabolcs Csepregi - Director of Search Technologies Structure search, JChem Base & Cartridge, Markush Project Akos Papp – Head of Chemical Registration Project

Product Development Calculator Plugins Zsolt Mohacsi,Nora Mate IUPAC Naming: Daniel Bonniot, Rita Vereb Automatic 3D Molecular Structure Generation: Odon Farkas, Imre Gabor, Adrian Kalaszi, Imre Jakli, Attila Szabo, Laszlo Antal Protonation, Partitioning, Charge, Isomers: Jozsef Szegezdi Marvin Ferenc Csizmadia Peter Csizmadia Andras Volford Tamas Vertse Erika Biro Judit Vasko-Szedlar Szilveszter Juhos Tamas Somogyvari Peter Vadasz

Product Development JChem Base Szabolcs Csepregi, Szilard Dorant, Edvard Buki, Tamas Csizmazia JChem Cartridge for Oracle Peter Kovacs Instant JChem Tim Dudgeon, Petr Hamernik Reactor, Standardizer, Metabolizer Gyorgy Pirok GUI : Istvan Cseh, Attila Szabo Engine: Zsolt Mohacsi, Nora Mate Libraries : Jeno Varga, Erzsebet Czinege, Gyorgy T. Balogh, Eszter Papp, Virag Sagi Kiss JKlustor, Screen, Fragmenter Miklos Vargyas LibMCS Miklos 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 stick JPG, PNG, SVG, Cut&Paste with Isis/ChemDraw, 2D cleaning, (de)aromatization, reaction drawing SDF, RDF, XYZ animations, CML, templates, compressed formats, Swing, 3D models 2001 Mac support, signed applets, Java Web Start, atom mapping Partial charge, pK a, 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, Tautomers, resonance, lone pairs, conformers, 3D sketching, MarvinSpace, Topology analysis, presentation quality graphics,... MarvinSketch/View MarvinSpace More Plugins, more R-groups, EMF, PDF and Mol2, Improved property storage in MRV, SDfiles and Rdfiles..NET support in MarvinBeans 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 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… JChem Base JChem Cartridge 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 MarvinSpace Calculator Plugins Structural Search JChem Base Instant JChem JChem Cartridge Standardizer Screen JKlustor Fragmenter Reactor

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