ChemAxon: Cheminformatics Solutions

1. Solutions for Cheminformatics Company and product overview April 2010

2. ChemAxon fingerprint Founded in 1998, based in Budapest, Hungary Database management tools, drug design and discovery Pharma, biotech, academia Representation in Europe,US, Japan, Indiaand China Wide industry reach >300corporate clients

3. Product Map

4. Active across the Globe

5. Active across the Globals

6. 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

7. GSK Case Study Adoption of full ChemAxon toolkit July 09. Replacing Daylight and ISIS globally Implementing Cartridge, IJC and JC4XL 3 months evaluation, 3 months pilot projects. Implementation ongoing – takes 12 months Choses ChemAxon for: Performance Ease of integration/implementation Flexible license model, includes partners Price (cost effectiveness)

8. 35 Integrator Partners Analysis and reporting Biological Data Management ELN Scientific Publishing Data Mining Workflow/pipeline tools Online Education SAR Laboratory Information Management Analytical chemistry Chemical inventory Chemical registration Sample management Patent search Toxicity and metabolites prediction

9. Applications integrating ChemAxon

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

11. Marvin Development History 1998 1999 2000 2001 2002 2003 Mac support, signed applets, Java Web Start, atom mapping SDF, RDF, XYZ animations, CML, templates, compressed formats, Swing, 3Dmodels SMILES, SMARTS, PDB, Rgroups, isotopes, shortcuts, Marvin Beans Ball and stickJPG, PNG, SVG, Cut&Paste with Isis/ChemDraw, 2D cleaning, (de)aromatization, reaction drawing Partial charge, pKa, logP/logD,3Doptimization, radicals,abbreviated groups Applets, Molfiles, stereo support, Windows, Unix 2007 2009 2006 2008 2004 2005 Transparent images .NET Applet loading speed up Sprout drawing Name to structure, OLE 2, Chemical Terms, Customizable GUI More Plugins, more R-groups, EMF, PDF and Mol2, Improved property storage in MRV, SDfiles and Rdfiles. .NET support in MarvinBeans. Structure to name, Coordination compounds, Polymer drawing, OLE, Markush enumerationplugin Configurations 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, Topologyanalysis,presentation quality graphics,...

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

13. Chemicalize the Web:http://www.chemicalize.org/ 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

14. JChem family

15. JChem development history 2000 2001 2002 2003 2004 Oracle, MySQL, SQLServer, Access, hashed fingerprints,substructure and similarity search Clustering, diversity DB2, PostgreSQL, Rgroup searching Reaction searching, fragmentation,reaction processing, standardization, pharmacophores, screening Cartridge, enhanced stereo searching, recursiveSMARTS,Chemical Terms, virtual synthesis 2005 2006 2009 2008 2007 Position variation queries, Instant JChem: • - Federated search, • - Cartridge support... Calculated columns, Installer, Tautomer Duplicate filtering, Query tables,Markush tables, Speed enhancementsforJChem Cartridge, form design, relational data for Instant JChem ... R-decomposition,R-enumeration, reaction library, custom fingerprints, random synthesis, link nodes… Tautomer search,Instant JChem reaction similarity, LibraryMCS, GUI for Standardizer/ Reactor … JChem for Excel JChem Web Services, AJAX Polymer search Data Sgroup search Faster SSS Metabolizer

16. 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 Searchhttp://www.chemaxon.com/Structural_Search.ppt JChem Base http://www.chemaxon.com/JChem_Base.ppt

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

18. 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 JChem Cartridge for Oracle

19. Instant JChem Instant JChem: http://www.chemaxon.com/conf/Instant_JChem.ppt 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 (106 +) • Dynamically predict properties using Calculator Plugins • Apply canonicalization rules for import and viewing • Wide import / export options • Merge data sets into a single set

20. JChem for Excel Microsoft Excel integrated solution for Marvin and JChem functionality Use Excel’s 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

21. 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

22. Standardizer http://www.chemaxon.com/Standardizer.ppt Canonicalization with Standardizer • 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

23. Drug discovery tools

24. Screen http://www.chemaxon.com/Screen.ppt Virtual Screening with Screen • 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)

25. JKlustor http://www.chemaxon.com/JKlustor.ppt Clustering with JKlustor • 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

26. Library profiling with Fragmenter Fragmenter 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 heteroatom (CCQ) • Functional groups remain intact • Very fast algorithm (no ring perception, no substructuresearch) • R-group decomposition

27. 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 thereaction engine for combinatorial chemistry. • Wizard-like applicationand reaction editor. • Built in testing system.

28. 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

29. Under Development • Integration of Screen descriptors and metrics into Cartridge • Structure Checker for Standardizer • New features for Instant JChem, like multi tier architecture, improved reporting capabilities, improved visualisation • Improve Markush structure handling in JChem Base / Cartridge / Marvin • 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

30. Visit othertechnical presentations MarvinSketch/Viewhttp://www.chemaxon.com/MarvinSketch_View.ppt MarvinSpacehttp://www.chemaxon.com/MarvinSpace.ppt Calculator Pluginshttp://www.chemaxon.com/Calculator_Plugins.ppt Chemical Naminghttp://www.chemaxon.com/conf/Naming.ppt Structural Searchhttp://www.chemaxon.com/Structural_Search.ppt JChem Basehttp://www.chemaxon.com/JChem_Base.ppt Markush Searchhttp://www.chemaxon.com/conf/Markush_development.ppt Instant JChemhttp://www.chemaxon.com/conf/Instant_JChem.ppt JChem for Excelhttp://www.chemaxon.com/product/jc4xl.html JChem Cartridgehttp://www.chemaxon.com/JChem_Cartridge.ppt Standardizerhttp://www.chemaxon.com/Standardizer.ppt Screenhttp://www.chemaxon.com/Screen.ppt JKlustorhttp://www.chemaxon.com/JKlustor.ppt Fragmenterhttp://www.chemaxon.com/Fragmenter.ppt Reactorhttp://www.chemaxon.com/Reactor.ppt

31. 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