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

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

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

Tautomerization Plugin

Resonance Plugin

Stereoisomer Plugin

Conformer Plugin

Molecular Dynamics Plugin

Geometry Plugin

Molecular Surface Area Plugin

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 conformers_at_ph.sdf idDistance …

Display Results In MarvinSpace

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

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 – plugins.html Unlimited predictions online – Plugin development – API documentation –