Solutions for Cheminformatics April 2010 Company and product overview

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

Product Map

Active across the Globe

Active across the Globals

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

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)

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

Applications integrating ChemAxon Target Identification Hit Generation Lead Generation Lead Optimization Knowledge database and management ELN Scientific Publishing Data Mining/ Analysis/ Visulisation Workflow/pipeline tools LIMS Chemical inventory Chemical registration Sample management SAR analysis Toxicity and metabolites prediction, ADMET

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 MarvinSpace

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, 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 enumeration plugin Configurations 2008 Name to structure, OLE 2, Chemical Terms, Customizable GUI 2009 Transparent images.NET Applet loading speed up Sprout drawing

Calculator Plugins Calculator Plugins 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.

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 Chemicalize the Web:

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…

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 R-decomposition, R-enumeration, reaction library, custom fingerprints, random synthesis, link nodes… 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 Position variation queries, Instant JChem: - - Federated search, - - Cartridge support JChem for Excel JChem Web Services, AJAX Polymer search Data Sgroup search Faster SSS Metabolizer

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 JChem Base

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:

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

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:

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

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

Canonicalization with Standardizer 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

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

Virtual Screening with Screen 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)

Clustering with JKlustor 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

Library profiling with Fragmenter Fragmenter 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

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.

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

Under Development Integration of Screen descriptors and metrics into Cartridge Structure Checker for Standardizer New features for Instant JChem, l ike 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

Visit other technical presentations MarvinSketch/View MarvinSpace Calculator Plugins Chemical Naming Structural Search JChem Base Markush Search Instant JChem JChem for Excel JChem Cartridge Standardizer Screen JKlustor Fragmenter Reactor

Find out more Product descriptions & links Forum Presentations and posters Download