1. UGM, June, 2007 Presenting: Szabolcs Csepregi JChem Base and Cartridge latest

2. Contents New in JChem Base & Cartridge architecture Search feature improvements Cartridge-specific news Future plans & development discussions Notations: – already released (available in latest version) – available to try out in alpha version

3. New in JChem Base & Cartridge Table types introduced: –Molecule –Reaction –Any structure –Markush –Query Reaction similarity for reaction tables

4. New in JChem Base & Cartridge Chemical Terms (calculated) columns –Example: asymmetricAtomCount()+3*ringCount() +0.5*logP() –Can use all CXN calculations + mathematical & logical operators –Automatically updated when structure inserted or updated –Search with Chemical Terms filter uses stored sub- expressions from CT columns

5. New in JChem Base & Cartridge Fingerprint statistics on table easier tuning for search speed (see speed tuning presentation last year)

6. New in JChem Base & Cartridge Installer Sortable chemical formula column (Proper sorting of numbers, not alphanumeric) JSP example enhancements –Display options (partial clean, handling of alignment & hit coloring) –More search options (ignore stereo, charge, isotope, vague bond options, etc.) –Markush tables: enumeration controls Progressive return of search hits (hits are returned during search) – provides improved speed!

7. New in JChem Base & Cartridge API (programming interface) improvements: Hit coloring and alignment Unified search options of database and in-memory search Custom atom & bond comparators to modify search behaviour (for advanced usage) Examples: –Define your own extra stereochemistry rules –Also consider atom maps, atom values, etc

8. New search features Component, mixture and formulation (ordered mixture) brackets Reacting center bond query feature (Search for changing, unmodified, etc. bonds during reaction search.)

9. New search features New query atom types Representation: Pseudo atoms (See More dialog in Marvin or the Beilstein generics dialog in ISIS/Draw) Query atom typeDescription AHAny atom type, including H QHHeteroatom or H MMetal MHMetal or H XHalogen XHHalogen or H GnMember of group (column) n in the periodic system (n = 1..18, G17 is the same as X)

10. Cartridge-specific news Optional CLOB storage of structure as structure column type ("US-ASCII" encoding only) jcf package ( overloaded functional equivalents, replaces old jcf_... functions) Partitioned JChem index Providing cost estimations to Oracle optimizer JChem Server improvement: HTTP(Tomcat) replaced by RMI to reduce communication overhead & simpler installation Speed enhancements –HTTP(Tomcat) -> RMI –Early return of first hits

11. Instant JChem released Easy-to-setup, easy-to-use GUI Most of JChem Base functionality available Access of remote JChem Base databases for: –Administration –Data entry & import –Searching & browsing –Sharing data See separate lecture later today

12. Future plans & discussions Next major version (Q3 2007): Coordination compounds insert and search Easier installation of Cartridge Database field access from Chemical Terms expressions Tautomer duplicate filtering option

13. Future plans & discussions Later major version (during next year): Pharmacophore query types (customizable pharmacophore point types of Screen) 3D searching (all conformers or multiple conformations) Parent search (ignore stereo and search only largest fragment) Chemical formula search with formula query language Web service interface for JChem Server Computational cluster support Start to extend Markush tool to patent area (longer term – will be discussed in detail tomorrow) Integration of Screen descriptors with Cartridge...?

14. Further info JChem Base resources http://www.chemaxon.com/product/jc_base.html http://www.chemaxon.com/product/jc_base.html JChem Cartridge resources http://www.chemaxon.com/product/jc_cart.html http://www.chemaxon.com/product/jc_cart.html Instant JChem resources http://www.chemaxon.com/product/ijc.html http://www.chemaxon.com/product/ijc.html Forum topics: –JChem Base, Cartridge & Searching: Home -> Forums -> Support -> Structure search and chemical database Home -> Forums -> Support -> Structure search and chemical database –Instant JChem: Home -> Forums -> Support -> Instant JChem Home -> Forums -> Support -> Instant JChem