1. Integrating JChem and Marvin into the Integrity ® Drug Discovery and Development Portal Rosa Alentorn, Gerard Chiva and Ann Wescott ChemAxon UGM, 7-8 June 2006

6. Why ChemAxon? Modern technology Java-based Ease of technical integration Ease of use of tools by end users – both internal and clients ChemAxon's responsiveness

7. Challenges encountered Technical Chemistry Workflow

8. Challenges encountered Technical Minimal problems were found by our technical staff as they worked to implement JChem and Marvin both in-house and in our products

9. Challenges encountered Chemistry Peptides "Any" search using Marvin applet Stereochemistry Salts Tautomers

10. Challenges encountered Workflow Searches retrieved "too many" compounds, requiring manual review and excessive time investment

11. Solutions Technical Chemistry Workflow

12. Solutions Technical Technical issues were resolved via contact with ChemAxon staff

13. Solutions Chemistry / Workflow Peptides, "any" search – v. 3.1.5 Stereochemistry, salts – Standardizer tool

14. Before v. 3.1.5 Peptides v. 3.1.5

15. Without Standardizer Search for isomers, ionic salts and solvates of ketoprofen

16. Without Standardizer Searching by substructure retrieves 70 structures, many of which are "not desired," for example:

17. Standardizer Designed to recognize the same compound represented with different chemical forms In Prous Science databases, also used to recognize salts, solvates, isomers, tautomers, etc., of the same compound with a single search

18. Carboxylates ClearStereo Fragment removal Ex: Ketoprofen derivatives

19. - >[O:1]=[C:2][#6:3]" /> >[C:1][O:2]" /> >[N]" /> >[N:2][C:1]" /> >[O:1]=[N:2][#6:3]" /> >[I:1]" /> >[F:1]" /> >[C:1]" /> >[In:1]" /> >[Tc:1]" /> Standardizer configuration

20. Chemical structures are stored "as drawn" and in standardized form Users can choose to search using the standardized structure or not Search results display the chemical structure "as drawn" Using "Standardized" structure

21. With Standardizer Search for isomers, ionic salts and solvates of ketoprofen

22. 10 structures retrieved, all desired, for example (1-6):

23. 10 structures retrieved, all desired, for example (7-10):

24. Wish List Greater ease in version upgrades JChem Manager with enhanced user friendliness Ability to display long lists of structures Tautomers Markush storage + retrieval capabilities

25. Next Steps Investigate how to use Standardizer to transform tautomers Implement Standardizer in end- user products Continue open communication with ChemAxon