1. Solutions for Cheminformatics September 2009 Company and product overview

2. ChemAxon fingerprint Founded in 1998, based in Budapest, Hungary Representation in Europe, US, Japan and China Wide industry reach >320 corporate clients >2600 Academic Package subscribers Wide expertise, critical mass (~50 staff) 15 PhD, 35 MSc

3. Product Map

4. Active across the Globe

5. Active across the Globals

6. ChemAxon Embedded - examples Workflow –Pipeline Pilot, InforSense KDE, and KNIME ELN –Agilent, Contur, DeltaSoft, Kinematik, etc. SAR –Spotfire, Synaptic Science, Omniviz Databases –Aureus, GVK, Jubilant Biosys Registration System –Patcore, Deltasoft Web content –Thomson Reuters, Wiley, Houghton Mifflin, Cengage, Prentice Hall, Collaborative Drug Discovery, RCSB PDB, BindingDB, NIH/NLM ChemIDPlus, Molport etc.

7. The ChemAxon Advantage Comprehensive –Visualisation /drawing, data management, drug discovery –From toolkit to fullkit Compatible –Mutliple platform support on all products –Customizable to own needs –API – Java,.NET, SOAP –Common core across all products Interface –Intuititive as you like it GUI –Easy to adopt/adapt Performance –Scalability –Speed Quality –Best in class products –Customer developed and tested Support –Rapid response (within 24 hr) –Project and integration management Experience –11 years cheminformaniacs –Development projects with biotech, chem services and publishers –Dozen successful migration projects

8. The Marvin family MarvinSketchMarvinViewMarvinSpace Available as applets for HTML pages and components for standalone apps (full API) Structure, query & reaction editing Individual and structure table visualization Macromolecule visualization MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt http://www.chemaxon.com/MarvinSketch_View.ppt MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt http://www.chemaxon.com/MarvinSpace.ppt

9. 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 20001999 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, 2004 2003 2005 Tautomers, resonance, lone pairs, conformers, 3D sketching, MarvinSpace, Topology analysis, presentation quality graphics,... 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, Coordination compounds, Polymer drawing, OLE, Markush enumeration plugin Configurations 2008 Name to structure, OLE 2, Chemical Terms, Customizable GUI 2009 Transparent images.NET Applet loading speed up Sprout drawing

10. Calculator Plugins Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppt http://www.chemaxon.com/Calculator_Plugins.ppt Elemental Analysis Structure to Name Protonation pKa, Major Microspecies, Isoelectric Point Partitioning logP, logD Charge Charge, Polarizability, Orbital Electronegativity Isomers Tautomerization,Resonance, Stereoisomer Conformation Conformer, Molecular Dynamics, 3D Alignment Geometry Topology Analysis, Geometry, Polar Surface Area (2D), Molecular Surface Area (3D) Markush enumeration Other Hydrogen Bond Donor-Acceptor, Huckel Analysis, Refractivity, Structure Frameworks Structure based calculations are available from the Marvin and Instant JChem GUI, cxcalc command line tool and the API/ Available as functions of Chemical Terms expressions.

11. Chemical Naming Structure to Name/ Name to structure Supported nomenclatures : Chains, Monocycles/ Traditional names with and without heteroatom/ Spiro ring systems/ Ethers/ Common characteristic groups, Ionic compounds/ Unlimited number of atoms and rings/ All atom types /Stereochemistry/ etc. Usage: drag&drop or copy&paste to MarvinSketch Label updated in real-time Automatic format recognition Batch from command line Name to structure conversion of documents www.chemicalize.org Chemicalize the Web: http://www.chemicalize.org/ http://www.chemicalize.org/

12. JChem family JChem BaseJChem CartridgeInstant JChemJChem for Excel API for structure searching and database handling Tight Oracle SQL integration Desktop application for scientist Marvin and JChem functionality Available from Java,.NET and Web services SQL functions for chemistry Access local and remote databases Excel functions, sorting, filtering, charge etc…

13. 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 R-decomposition, R-enumeration, reaction library, custom fingerprints, random synthesis, link nodes… 20052006 Tautomer search, Instant JChem reaction similarity, Library MCS, GUI for Standardizer/ Reactor … 2007 Calculated columns, Installer, Tautomer Duplicate filtering, Query tables, Markush tables, Speed enhancements for JChem Cartridge, form design, relational data for Instant JChem... Cartridge, enhanced stereo searching, recursive SMARTS, Chemical Terms, virtual synthesis 2004 2008 Position variation queries, Instant JChem: - - Federated search, - - Cartridge support... 2009 JChem for Excel JChem Web Services, AJAX Polymer search Data Sgroup search Faster SSS Metabolizer

14. Features Fast and sophisticated searching ( chemical and non-chemical data, Chemical Terms filter, many options ) Custom standardization Calculated columns Combinatorial Markush structure tables Interfaces Integration with most relational database engines JChem Cartridge for tight Oracle SQL integration JSP and AJAX open source web examples Desktop-ready through Instant JChem JChem Web Services available JChem Base DB2 Structural Search http://www.chemaxon.com/Structural_Search.ppt http://www.chemaxon.com/Structural_Search.ppt JChem Base http://www.chemaxon.com/JChem_Base.ppt http://www.chemaxon.com/JChem_Base.ppt

15. Searching in combinatorial Markush structures Combinatorial Markush structure registration and search Markush features handled in search & enumeration: R-groups (nesting to any depth) Atom lists, bond lists Position variation bond Link nodes and repeating units Homology groups Compatible Markush enumeration pluginMarkush enumeration plugin Not all query features supported Detailed description: http://www.chemaxon.com/product/markush_search.html

16. JChem Cartridge for Oracle Access JChem functionality via SQL functions All search features of JChem Base JChem index for chemical data in arbitrary database structure Chemical filters and property predictors using Chemical Terms Standardization (structure canonicalization) during registration Structure format conversions 2D, 3D image generation Library enumeration using virtual reactions and Markush structures JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt http://www.chemaxon.com/JChem_Cartridge.ppt

17. Instant JChem Desktop application for local and remote chemical database management, search and structure based prediction Simply connect to external databases and share your native database simultaneously Powerful search functionalities Scalable – explore large datasets (10 6 +) Dynamically predict properties using Calculator Plugins Apply canonicalization rules for import and viewing Wide import / export options Merge data sets into a single set Instant JChem: http://www.chemaxon.com/conf/Instant_JChem.ppt

18. JChem for Excel Microsoft Excel integrated solution for Marvin and JChem functionality Use Excels powerful features: Functions, Sorting, Filtering, Charts… Implemented in C#.NET, and Visual Studio –Proof that ChemAxon APIs can be used in a Java-less.NET environment Easy to install and deploy

19. JChem Web Services Server Web Services integration of JChem functionality JChem Search Molecular Conversion Standardizer Chemical Terms Enables SOAP capable (e.g. AJAX, Perl, Python) programming environments Standalone server Chainable with other web services Easy to install and deploy

20. Canonicalization with Standardizer Standardizer http://www.chemaxon.com/Standardizer.ppt http://www.chemaxon.com/Standardizer.ppt Structure canonicalization –Mesomers –Tautomers –Solvent and counter ion removal –Aromatization, dearomatization –Explicit/implicit hydrogen conversion –Stoichiometry expansion –Stereo manipulations –2D cleaning –Template based cleaning Custom rules Structure checker Availability –JChemBase –API –Batch processing

21. Drug discovery tools JKlustorScreen Profiling, analysis, diversityVirtual screening by topological descriptors FragmenterReactor Library profiling and reactant generation Virtual reactions and synthesis

22. Virtual Screening with Screen Screen http://www.chemaxon.com/Screen.ppt http://www.chemaxon.com/Screen.ppt Active set dependent automated optimization Wide range of descriptors –native chemical fingerprint –pharmacophore fingerprint customizable definitions functional group based mapping calculation based mapping –calculator plugins –user defined descriptors –combined descriptors Tanimoto and Euclidean metrics –Tunable parameters normalization weighting scaling directing (asymmetric)

23. Clustering with JKlustor JKlustor http://www.chemaxon.com/JKlustor.ppt http://www.chemaxon.com/JKlustor.ppt Similarity and structure based, Hierarchical and non-hierarchical methods –hierarchical Ward MCS –non-hierarchical Jarvis-Patrick Wide range of descriptors –Chemical fingerprint –Pharmacophore fingerprint –Calculator plugins –User defined custom descriptors

24. Library profiling with Fragmenter Fragmenter http://www.chemaxon.com/Fragmenter.ppt http://www.chemaxon.com/Fragmenter.ppt Transformation based fragmentation method –Customizable transformations –RECAP transform set –Synthetically relevant transformations –Labeled connections –Options to keep fragment feasible (no ring opening, limit fragment size, limit the number of connection points, etc) –Fragment statistics –Activity based scoring High throughput fragmentation Simple rule cleaving carbon-carbon single bond next to a hetero atom (CCQ) Functional groups remain intact Very fast algorithm (no ring perception, no substructure search) R-group decomposition

25. Virtual Synthesis with Reactor Reaction Engine –Converts reactants according to a given reaction scheme –Chemo-, regio- and stereospecific reactions are supported by the integrated property calculation functions (if the reaction contains rules in Chemical Terms format). –Compatible with the popular molecule, reaction file and reaction mapping formats. Reactor Application –An application of the reaction engine for combinatorial chemistry. –Wizard-like application and reaction editor. –Built in testing system.

26. Metabolizer Virtual reaction based metabolite enumeration tool xenobiotic metabolic pathways prediction metabolic stability metabolically sensitive groups and major metabolites can be customized by various biotransformation libraries Human phase I, xenobiotic CYP450 biotransfomation library UNDER DEVELOPMENT

27. Under Development Integration of Screen descriptors and metrics into Cartridge Structure Checker for Standardizer Marvin GUIs to be added to the.Net API New features for Instant JChem, l ike multi tier architecture, improved reporting capabilities, improved visualisation Improve Markush structure handling in JChem Base / Cartridge / Marvin JChem for Excel Metabolite and metabolic stability prediction Human CP450 biotransformation library Multistep reactions in Marvin and JChem Compound registration system 3D similarity searching based on flexible alignment SKC support

28. Visit other technical presentations MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt http://www.chemaxon.com/MarvinSketch_View.ppt MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt http://www.chemaxon.com/MarvinSpace.ppt Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppthttp://www.chemaxon.com/Calculator_Plugins.ppt Chemical Naming http://www.chemaxon.com/conf/Naming.ppt http://www.chemaxon.com/conf/Naming.ppt Structural Search http://www.chemaxon.com/Structural_Search.ppthttp://www.chemaxon.com/Structural_Search.ppt JChem Base http://www.chemaxon.com/JChem_Base.ppt http://www.chemaxon.com/JChem_Base.ppt Markush Search http://www.chemaxon.com/conf/Markush_development.ppt http://www.chemaxon.com/conf/Markush_development.ppt Instant JChem http://www.chemaxon.com/conf/Instant_JChem.ppthttp://www.chemaxon.com/conf/Instant_JChem.ppt JChem for Excel http://www.chemaxon.com/product/jc4xl.htmlhttp://www.chemaxon.com/product/jc4xl.html JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt http://www.chemaxon.com/JChem_Cartridge.ppt Standardizer http://www.chemaxon.com/Standardizer.ppt http://www.chemaxon.com/Standardizer.ppt Screen http://www.chemaxon.com/Screen.ppt http://www.chemaxon.com/Screen.ppt JKlustor http://www.chemaxon.com/JKlustor.ppt http://www.chemaxon.com/JKlustor.ppt Fragmenter http://www.chemaxon.com/Fragmenter.ppt http://www.chemaxon.com/Fragmenter.ppt Reactor http://www.chemaxon.com/Reactor.ppt

29. Find out more Product descriptions & links www.chemaxon.com/products.html Forum www.chemaxon.com/forum Presentations and posters www.chemaxon.com/conf Download www.jchem.com/licensefrset.html