1. Java Solutions for Cheminformatics Feb 2008 Whats new for PP

2. CXN Toolkit and applications overview

3. In action: MarvinView and MarvinSketch

4. In action: Calculator Plug-ins

5. Chemical Terms

6. 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 integration – open source web example Desktop-ready through Instant JChem Structure management and search in JChem Base DB2

7. JChem Database Search Several search options were added Easier protocol integration and better performance due to concentrated functionality

8. Canonicalization with Standardizer Aromatize/dearomatize Add/remove explicit hydrogens Convert mesomers / tautomers / functional groups Remove solvents counterions by list smallest fragment retain largest fragment Set/Remove chiral flag, remove stereo features Ungroup S groups Enumerate by stoichiometry values 2D, 3D coordinate generation (cleaning) Template based cleaning

9. Canonicalization with Standardizer Simple to use, but now full complexity is also available: Simple actions (checkboxes) Configuration string (simple or XML) Configuration file

10. Virtual Synthesis with Reactor Effective focused, combinatorial and diverse libraries combinatorial, random and exhaustive dispatching high throughput Flexible memory, file and database operations sequential or combinatorial mode compound or reaction output type reverse direction Compatible –reactions: MRV, RXN, RDF, SMARTS/SMIRKS –compounds: MRV, MOL, SDF, SMILES –mapping: ChemAxon, Daylight, automapper Smart –chemo-, regio- and stereospecific –customizable

11. Combinatorial Reactor Example

12. Instant JChem as PP file viewer Use Pipeline Pilot to create and update databases that can be intuitively searched and analyzed using Instant JChem Simple connect to external databases and share your native database simultaneously Powerful search functionalities Scalable – explore 00,000s+ live structures Dynamically predict properties using Calculator Plugins Apply canonicalization rules for import and viewing Wide import & export options / Merge data sets into a single set Form building, analysis & Reporting Java Web Start and API simplify deployment enterprise wide

13. Current developments - node building support New nodes to support current ChemAxon functionality More compatibility with existing nodes/functionality Support for newer functionality more quickly Support for PP nodes from ChemAxon directly ChemAxon took over responsibility for building and supporting ChemAxon toolkit Pipeline Pilot nodes from Scitegic.

14. Available components –Standardizer –Chemical Terms expressions –Reactor –JChem chemical database: insertion, search and retrieval of structures –Calculator plugins (HBA, HBD, Isoelectric point, logP, logD, pKa, Polarizability, Refractivity, TPSA) –Marvin sketcher and viewer –Major microspecies (major protonation form) –Microspecies distribution –Burden eigenvalue descriptor (BCUT)

15. Planned components –JChem Cartridge for Oracle –Instant JChem end user desktop cheminformatics solution –Name to structure, structure to name generation –Tautomer and conformer generation –Conversion of various structure file formats –MCS based clustering Node release cycle is fast and flexible. Please advise us on priority and additional functionality for future node development.

16. Under development - general Marvin new framework = prettier, multiple skins, more customizable for users and developers 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 Multi-step reactions in Marvin and JChem Virtual Synthesis Module for Instant JChem Application for compound registration system QSAR based on 3D conformers

17. Find out more Product descriptions & links –www.chemaxon.com/products.htmlwww.chemaxon.com/products.html Forum –www.chemaxon.com/forumwww.chemaxon.com/forum Presentations and posters –www.chemaxon.com/confwww.chemaxon.com/conf Download JChem/Marvin and nodes –http://www.chemaxon.com/download.htmlhttp://www.chemaxon.com/download.html