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Advanced Java Solutions for Cheminformatics: New Plugins for Structure-Based Predictions

This document discusses innovative Java solutions and new plugins developed by Zsolt Mohácsi and colleagues for cheminformatics to enhance structure-based predictions. It highlights the functionalities and integration of the UGM Calculator Plugin Interface with Marvin GUI, incorporating various tools for chemical analysis such as pKa, logP, stereoisomer analysis, and molecular dynamics. These plugins simplify the process of molecular modeling and predictions, allowing researchers to derive insights into chemical properties efficiently through versatile Java APIs.

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Advanced Java Solutions for Cheminformatics: New Plugins for Structure-Based Predictions

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  1. Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté,József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli June2006, UGM

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

  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 id Distance 1 7.86 2 9.08 3 7.15 4 8.06 5 8.54 6 8.52 7 6.24 8 7.07 9 7.48 10 3.33 11 6.31 12 4.14 13 4.79 14 3.26 …

  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

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