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 15-16 conformers_at_ph.sdfid Distance1 7.862 9.083 7.154 8.065 8.546 8.527 6.248 7.079 7.4810 3.3311 6.3112 4.1413 4.7914 3.26…

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

– 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