1. Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli June 2006, UGM

2. Calculator Plugin Interface Marvin GUI cxcalc command line tool Java API Chemical Terms evaluate command line tool search filtering JChem Cartridge reaction processing

3. New Plugins Elemental Analysys Protonation –pKa, Major Microspecies, Isoelectric Point Partitioning –logP, logD Charge –Charge, Polarizability Isomers –Tautomers, Resonance, Stereoisomers Conformation –Conformers, Molecular Dynamics Geometry –Topology Analysis, Geometry, Polar Surface Area, Molecular Surface Area Other –H Bond Donor/Acceptor, Huckel Analysis, Refractivity

4. Tautomerization Plugin

5. Resonance Plugin

6. Stereoisomer Plugin

7. Conformer Plugin

8. Molecular Dynamics Plugin

9. Geometry Plugin

10. Molecular Surface Area Plugin

11. Using New Plugins With cxcalc Calculate 400 conformers at pH=7.4 of molecule m1 (using major microspecies and conformer plugin): $ cxcalc majorms -H 7.4 -f mol m1.mol | cxcalc conformers -m 400 -f sdf > conformers_at_ph.sdf Calculate the distance of atom 15 and atom 16 in each conformer (using geometry plugin): $ cxcalc distance –a 15-16 conformers_at_ph.sdf idDistance 17.86 29.08 37.15 48.06 58.54 68.52 76.24 87.07 97.48 103.33 116.31 124.14 134.79 143.26 …

12. Display Results In MarvinSpace

13. Use MarvinSpace Display In Custom Plugins plugin.getResultDomain(Object) == CalculatorPlugin.ATOM plugin.getResult(Object, int) instanceof Number

14. Acknowledgements, Links Acknowledgements ChemAxon people taking part in development: –Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli (plugin development) –Judit Papp, Miklós Vargyas (MarvinSpace) Links Calculator plugins –www.chemaxon.com/marvin/chemaxon/marvin/help/calculator- plugins.html Unlimited predictions online –www.chemaxon.com/demosite/marvin/index.html Plugin development –www.chemaxon.com/marvin/doc/dev/plugins.html API documentation –www.chemaxon.com/marvin/doc/api/index.html