1. version 5.3, February 2010 Scientific & technical presentation JChem Base

2. Introduction to JChem Base High performance Java based tools for: storage, search and retrieval of chemical structures and associated data The components can be integrated into web-based or standalone applications in association with other ChemAxon tools

3. Structural overview Web browser Application Web application JChem Base API: Chemical logic Structure cache JDBC driver: Standard interface to the RDBMS RDBMS (e.g. Oracle, MySQL, etc.) : Storage and security

4. Compatibility and integration File formats: SMILES MDL molfile (v2000 and v3000) MDL SDF RXN RDF MRV IUPAC name, InChI Markush DARC CDX Integration: extensive API for Java.NET JChem Cartridge for Oracle Database engines: Oracle MySQL MS SQL Server PostgreSQL MS Access IBM DB2 Derby etc. Operating systems: Windows Linux Mac OS X Solaris etc.

5. JSP example application Features: Substructure, Superstructure, Full, Exact fragment, Similarity and Perfect search Molecular Descriptor similarity search with descriptor coloring Substructure hit alignment and coloring, inverse hit list Chemical Terms filter Import / Export Export of hits Insert / Modify / Delete structures AJAX in JChem Webservices

6. Structure search features See detailed information on structure search: www.chemaxon.com/conf/Structural_Search.ppt Wide range of query atoms Query properties R-group queries Full SMARTS support Coordination compounds Link nodes Pseudo atoms, lone pairs Relative stereo Reaction search features Hit coloring, position variation Polymers

7. Search options Some selected structure search options: Stereo on/off Ignore charge/isotope/radical/ valence/polymers, etc. Vague bond matching options Chemical Terms filter Tautomer search Inverse hit list Maximum search time / number of hits Combine with non-structure conditions Ordering of results etc.

8. JChem Base 5.2.2, Intel Quad Q6600 2.4GHz, 8 GB RAM; Oracle 10.2.0.3 Performance (1) Number of compounds Elapsed time Duplicates not checked Duplicates checked 10,00021 s26 s 100,0002 min 4 s2 min 34 s 200,0004 min 24 s5 min 13 s QueryNumber of hitsSearch time 20.91 s 930.98 s 6,0011.30 s 146,2565,66 s Compound registration: Substructure search in PubChem (19.5 million compounds):

9. Performance (2) Similarity search: Tanimoto >0.9 JChem Base 5.2.2, Intel Quad Q6600 2.4GHz, 8 GB RAM; Oracle 10.2.0. QueryNumber of hitsSearch time 03.39 s 03.82 s 03.33 s

10. Markush structures Markush structure registration and search Markush features R-groups Atom lists, bond lists Position variation bond Link nodes and repeating units Homology variation (alkyl, aryl, etc.) Compatible Markush enumeration plugin

11. Administration with JChemManager User interface for creating tables import export deleting rows dropping tables Most functions are also available from command line.

12. Standardization Default standardization includes: – Hydrogen removal – Aromatization Custom standardization can be specified for each table by specifying an XML configuration file at table creation or in the Table Options dialog of JChem Manager (jcman)

13. Custom Standardization Example afterbefore Standardizer http://www.chemaxon.com/conf/Standardizer.ppt http://www.chemaxon.com/conf/Standardizer.ppt

14. The property table The property table stores information about JChem structure tables, including: Fingerprint parameters Custom standardization rules Other table options and information More than one property table can be used, each property table represents a particular JChem environment.

15. Table types Control allowed chemical structures and available operations Molecule Reaction Markush Query Any structure

16. The structure of JChem tables Column nameExplanation cd_idunique numeric identifier in the table cd_structure the imported structure in the original format, without modifications (except for the removal of data fields) cd_smiles; cd_smarts; cd_markush the standardized structure format dependig on the different table types, used by the search process cd_formulathe formula of the standardized structure cd_sortable_formulaformula representation for alphanumerical sorting cd_molweightthe molecular weight of the standardized structure cd_hash; cd_flags; cd_fp… fields used internally for structure searching cd_timestampthe date and time of the insertion of the row [user fields]custom data fields can be added by the user

17. Structural search in database Two stage method provides optimal performance: 1. Rapid pre-screening reduces the number of possible hit candidates Chemical Hashed Fingerprints are used for substructure and superstructure searches Hash code is used for duplicate filtering (usually during compound registration) 2. Graph search algorithm is used to determine the final hit list

18. Structure Cache Contains Fingerprints for screening and ChemAxon Extended SMILES for ABAS Instant access to the structures for the search process Reduced load on the database server Incremental update ensures minimum overhead after changes in the table Small memory footprint due to –SMILES compression –Optimized storage technique Approximately 100MB memory needed for 1 million typical drug-like structures (using default, 512 bit long fingerprints)

19. Future plans Graphical user interface for R-group decomposition Arbitrary table structure (Java and.NET API for JChem index) Maximum common substructure search type Additional layer: JChem Server (later also as grid) Compound registration system API

20. Summary ChemAxons JChem Base API provides sophisticated high performance tools for the developer to deal with chemical structures and associated data. Building on the JChem API is convenient, because: Our various tools integrate seamlessly Both high and low level API classes are available Responsive developer-to-developer support

21. Links JChem home page: http://www.chemaxon.com/products/jchem-base Online tryout: http://www.chemaxon.com/jchem/examples.html API documentation: http://www.chemaxon.com/jchem/doc/api/index.html Brochure: www.chemaxon.com/brochures/JChemBase.pdf

22. 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.ppt http://www.chemaxon.com/Calculator_Plugins.ppt JChem Base http://www.chemaxon.com/JChem_Base.ppt http://www.chemaxon.com/JChem_Base.ppt 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 http://www.chemaxon.com/Reactor.ppt