1. Scientific & technical presentation Standardizer January 2008

2. Why standardize structures? To recognize the same compound represented with different chemical forms

3. Custom transformations Built-in functions Availability

4. Mesomers

5. Tautomers oxo-enol, enamine-imine

6. Tautomers pyridone-pyridol

7. Solvent removal

8. Specific counterion removal

9. Built-in functions Custom transformations Built-in functions Availability

10. Fragment removal

11. Aromatization

12. Dearomatization

13. Hydrogen conversions converting implicit hydrogens to explicit

14. Hydrogen conversions converting explicit hydrogens to implicit

15. 2D Cleaning

16. Template-based Cleaning 2D-coordinate calculation of macrocycles or bridged systems

17. query Template-based Cleaning aligning search results to the query

18. Stereo manipulations removing absolute R/S and E/Z stereo configurations

19. Stereo manipulations setting the absolute stereo (chiral) flag for stereo molecules

20. Stoichiometry expansion expanding reaction stoichiometry

21. Stoichiometry expansion expanding salt stoichiometry

22. Group manipulation

23. Availability Custom transformations Built-in functions Availability

24. API and command line interface Standardizer st = new Standardizer(new File("standardize.xml")); st.standardize(mol); standardize input.sdf -c config.xml -o output.smiles

25. Graphical User Interface

26. Features General –aromatize/dearomatize –add/remove explicit hydrogens Transforms –mesomers –tautomers –functional groups Removals –solvents –counterions by list –remove smallest fragment –keep largest fragment –R-groups Stereo –remove stereo features –set the absolute stereo flag Sgroups –expand/contract/ungroup –clear/set the absolute stereo flag –expand stoichiometry of attached data Cleaning –partial –full –template based

27. Features Compatible –MOL, SDF, RXN, RDF (V2000/V3000) –SMILES, SMARTS/SMIRKS (recursive too) –MRV, CML, PDB Flexible –customizable parameters –customizable conversions Available –full API –command line interface –integration with JChem Base and Cartridge –documentation and examples –free for the Academic community

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