1. Standardizer Molecular Cosmetics for Chemoinformatics György Pirok Java Solutions for Cheminformatics

2. Why standardize structures? Canonicalisation Uniformization of structures without changing the chemical content to recognize duplicates, functional groups (aromatization, mesomers, tautomers,... ) Beautification Making the structures visually more attractive ( dearomatization, cleaning coordinates, wedge orientation,... ) Modification Conversion of structures by modifying its original content as a preparation step for further chemoinformatics tasks (transformations, removing stereo, removing R-groups,...).

3. Canonicalisation making hydrogens explicit converting to canonical mesomer form transforming to user defined mesomer form Hydrogens aromatizing Kekülé rings Resonant structures converting to canonical tautomer form removing user defined fragments transforming to user defined tautomer form Tautomers expanding stoichiometry Other removing small fragments making hydrogens implicit setting the chiral flag

4. Mesomers

5. Tautomers oxo-enol, enamine-imine

6. Fragment removal

7. Specific counterion removal

8. Solvent removal

9. Beautification calculating 2D coordinates Hydrogens converting aromatic rings to Kekülé format Resonant structures making hydrogens implicit Cleaning reallocating wedge bonds contracting/expanding/ ungrouping abbreviated and multiple groups Groups template based cleaning 3D geometry optimization

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

11. query Template-based Cleaning orienting search results to the query

12. client Canonicalization During Database Import Relational Database input structures canonicalization configurationoriginal structurescanonicalized structures server Standardizer JChem Base / Cartridge

13. client Sending Query to the Database Relational Database server query structure canonicalization configurationcanonicalized query query is compared to the canonicalized structures Standardizer JChem Base / Cartridge

14. Displaying Result Structures Relational Database original structures server client beautification configuration beautified structures Standardizer JChem Base / Cartridge

15. Modification custom transformations +

16. 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

17. Standardizer GUI

18. Applications: Virtual Synthesis

19. Applications: Structure Databases

20. Acknowledments Ferenc Csizmadia Nóra Máté István Cseh Szabó Attila Alex Allardyce Szilárd Dóránt Péter Kovács Szabolcs Csepregi Java Solutions for Cheminformatics