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WISDOM mini-workshop

WISDOM mini-workshop. Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) ISGC 2007 March 28th, 2007. Mini-workshop program. Introduction (V.B.) Analysis of the first data challenge on avian flu (Y-T Wu, Academia Sinica) Short term perspective: second data challenge on avian flu

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WISDOM mini-workshop

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  1. WISDOM mini-workshop • Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) • ISGC 2007 • March 28th, 2007

  2. Mini-workshop program • Introduction (V.B.) • Analysis of the first data challenge on avian flu (Y-T Wu, Academia Sinica) • Short term perspective: second data challenge on avian flu • Other perspectives • Knowledge repository for avian flu • New data challenges on neglected diseases

  3. Content • Brief presentation of the collaboration • Status • Membership • Status of the different data challenges • First data challenge on avian flu • First data challenge on malaria • Second data challenge on malaria

  4. WISDOM • Goal: contribute to develop new drugs for neglected and emerging diseases with a particular focus on malaria and avian flu • Specificity: extensively rely on emerging information technologies to provide new tools and environments for drug discovery and development. • Initial focus: screening • Web site: http://wisdom.healthgrid.org

  5. WISDOM collaboration Asian partners Non Asian partners Associated labs LPC Clermont-Ferrand: Biomedical grid SCAI Fraunhofer: Knowledge extraction, Chemoinformatics CEA, Acamba project: Biological targets, Chemogenomics Chonnam nat. univ.: In vitro testing Univ. Modena: Biological targets, Molecular Dynamics HealthGrid: Biomedical grid, Dissemination ITB CNR: Bioinformatics, Molecular modelling Academica Sinica: Grid user interface Biological targets In vitro testing Univ. Los Andes: Biological targets, Malaria biology Mahidol University Bangkok, Thailand: In vitro testing New Univ. Pretoria: Bioinformatics, Malaria biology 7 partners, 4 associated laboratories providing targets and/or in vitro facilities

  6. IT development activities • Groups involved: ASGC, CNRS and ITB-CNR • Development of a full grid-enabled virtual screening procedure (EGEE, Embrace, BioinfoGRID) • Docking + post-docking analysis • Molecular Dynamics + post-MD analysis • Development of a production environment (EGEE, Embrace, BioinfoGRID) • Secure storage of biochemical information in a database • WISDOM client using web service technology • Improved monitoring features • To do: workflow

  7. Status of WISDOM-I data challenge on malaria • Reminder • One target: plasmepsins II and IV • Docking software: FlexX • Compound library: ChemBridge (500.000 compounds) • Docking results completely analyzed (SCAI Fraunhofer) • Best 25000 compounds selected • Reranking of the selected compounds using MD (Univ. Modena, CNRS) • Best 200 compounds just selected • In vitro screening to start next month at Chonnam National University

  8. Status of WISDOM-II data challenge on malaria • Reminder • 4 targets: GST, tubulin, DHFR Pl. falciparum and vivax • Docking software: FlexX • Compound library: ZINC • Data challenge finished on Jan 31st • > 400 CPU years • Collection of data produced under way • Analysis to start soon • Tubulin: CEA Grenoble • GST: Univ. Pretoria • DHFR: Univ. Los Andes and Univ. Modena

  9. Second data challenge on avian flu: brainstorming • Focus: • Target(s) • Docking software • Compound library • Issues encountered with first data challenge • Production environment • New WISDOM environment • Docking workflow • Amount of resources needed • Timing

  10. Other issues for discussion • Relationship with PRAGMA • KISTI volunteering to develop API’s to deploy WISDOM on PRAGMA testbed • PRAGMA announced last week an initiative on avian flu • Focus on building a knowledge repository • Interest to collaborate ? • Perspectives on neglected diseases • Invitation to contribute to TDR initiative for the computational prioritization of candidate targets for neglected tropical diseases http://genoma.unsam.edu.ar/portfolio/ • Offer from WHO/TDR Drug Target Portfolio initiative to recommend targets for the next data challenge on neglected diseases

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