1. UGM, June, 2007 Szabolcs Csepregi Markush: Whats new, development discussions

2. Contents What is Markush, overview of earlier project Summary of current functionality Recent improvements Planned features towards patents Development discussions roundtable

3. What is Markush A description of compound classes by generic notations: –R-groups (substituent variation) –Atom, bond lists –Repeating units (link nodes and groups) –Position variation (variable point of attachment) –Homology variation (e.g. alkyl, aryl) –Conditions for generic features: occurrence lists, dependency, etc. Used for description of: –Patent claims –Combinatorial libraries Picture from Wikipedia:

4. ChemAxon Markush project Goals: –Extend structural search capabilites to combinatorial Markush structures –Markush enumeration Complications: –Practical examples may be very complex, methods using explicit enumeration may be impossible –Extension of current molecular formats (generic features) Pilot study started in 2005 Q4, first results were shown at UGM, 2006 June.

5. Summary of current functionalities Combinatorial Markush Markush features handled in search & enumeration: –R-groups –Atom lists –Bond lists –Link nodes Searching: considers all possibilities/definitions without explicit enumeration Can handle all search types, stereo, query atoms, bonds, query properties: a, R,,.

6. Recent improvements Special Markush tables in JChem Base (to register combinatorial Markush structures) Speed improvements in Markush registration and searching in database

7. Recent improvements - Enumeration Markush enumeration plugin –Full enumeration –Selected parts only –Random enumeration –Calculate library size: exact size of huge Markush libraries arbitrary precision or magnitude

8. Recent improvements - drawing Zoom to scaffold/selection Position variation (variable point of attachment) Repeating unit with repetition ranges

9. Planned features towards Patents New Markush features (drawing & search): Position variation (variable point of attachment) Homology variation (using predefined generic atoms - alkyl, aryl, etc.) –Properties (# of atoms, branching points, # of heteroatoms, etc.) Multiple attachment points of R-groups Repeating units with repetition range (repeating groups) Bridged definition of multiple R-atoms R1, R2= H, CH3, NO2 or together form a ring

10. Planned features towards Patents Search Markush structures in Markush tables (Markush on query side) –Is there an overlap between libraries? –What is the overlap?

11. Development discussions We plan to work closely with publishers during development to provide the right tools for patent Markush data. Are these tools or a combined offer (content + tools) useful for you or your organization? –What type of usage do you envision? – departments, types of usage –Portal vs. in-house installation? In-house or purchased data? etc. What other functionalities would you like to see? Interested in evaluation? –or providing test data?

12. Development discussions Thank you!