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WISDOM : Grid-enabled Virtual High Throughput Screening

WISDOM : Grid-enabled Virtual High Throughput Screening. N. Jacq LPC of Clermont-Ferrand (CNRS/IN2P3) Biomed meeting, Lyon, 2006/04/28. WISDOM : Wide In Silico Docking On Malaria. Partners Fraunhofer SCAI, Germany (Project PI: Martin Hofmann) LPC Clermont-Ferrand, France (CNRS/IN2P3)

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WISDOM : Grid-enabled Virtual High Throughput Screening

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  1. WISDOM : Grid-enabled Virtual High Throughput Screening N. Jacq LPC of Clermont-Ferrand (CNRS/IN2P3) Biomed meeting, Lyon, 2006/04/28

  2. WISDOM : Wide In Silico Docking On Malaria • Partners • Fraunhofer SCAI, Germany (Project PI: Martin Hofmann) • LPC Clermont-Ferrand, France (CNRS/IN2P3) • CMBA, France (Center for Bio-Active Molecules screening) • BioSolveIT • HealthGrid • Representing different projects: • EGEE (EU FP6) • Simdat (EU FP6) • AuverGrid (French Regional Grid) • Accamba project (French ACI project) WISDOM in EGEE-2, biomed meeting, 2006/04/28

  3. High Throughput Virtual Docking Chemical compounds (ZINC): Chembridge – 500,000 Drug like – 500,000 Millions of chemical compounds available in laboratories High Throughput Screening 1-10$/compound, nearly impossible Molecular docking (FlexX, Autodock) ~80 CPU years, 1 TB data Data challenge on EGEE ~6 weeks on ~1700 computers Hits screening using assays performed on living cells Hits refining Using Molecular Dynamics Targets (PDB): Plasmepsin II (1lee, 1lf2, 1lf3) Plasmepsin IV (1ls5) WISDOM in EGEE-2, biomed meeting, 2006/04/28

  4. Significant numbers • Total of 46 million ligands docked in 6 weeks • 1TB of data produced • Up 1700 computers in 15 countries used simultaneously • corresponding to about 72 000 jobs and 80 CPU years • Average crunching factor ~660 Number of running and waiting jobs vs time Number of running and waiting jobs vs time WISDOM in EGEE-2, biomed meeting, 2006/04/28

  5. country sites country sites country sites Bulgaria 3 Greece 3 Romania 1 Croatia 1 Israel 1 Russia 2 Cyprus 1 Italy 13 Spain 7 France 9 Netherlands 2 Taiwan 1 Germany 1 Poland 1 UK 10 Deployment on EGEE infrastructure, wisdom.eu-egee.fr Countries with nodes contributing to the data challenge WISDOM Total amount of CPU provided by EGEE federation WISDOM in EGEE-2, biomed meeting, 2006/04/28

  6. Data challenge on avian flu • A collaboration of 5 grid projects: Auvergrid, BioinfoGrid, EGEE-II, Embrace, TWGrid • Partners Institute : Academia Sinica (Computing Center, Genomics Research Center), CNRS-LPC, CNR-ITB • Timescale: • First contacts: March 1st 2006 • kick-off: April 1st 2006 • Duration: ~4 weeks WISDOM in EGEE-2, biomed meeting, 2006/04/28

  7. Data challenge on avian flu: biological goals • The bird flu virus is named H5N1. H5 and N1 correspond to the name of proteins (Hemagglutinins and Neuraminidases) on the virus surface. • Neuraminidases play a major role in the virus multiplication • Present drugs such as Tamiflu inhibit the action of neuraminidases and stop the virus proliferation • The virus keeps mutating and drug-resistant N1 variants can appear • The goal of the data challenge is to study in silico the impact of selected point mutations on the efficiency of existing drugs and to find new potential drugs H5 N1 Credit: Y-T Wu WISDOM in EGEE-2, biomed meeting, 2006/04/28

  8. Data challenge on avian flu: grid facts • Data challenge parameters: • One docking software: autodock • 8 conformations of the target (N1) • 300000 selected compounds • 100 year CPU to dock all configurations on all compounds Credit: Y-T Wu WISDOM in EGEE-2, biomed meeting, 2006/04/28

  9. Perspectives • Future works on the hits : reranking of WISDOM hits by Molecular Dynamics simulations • Approximately 100 CPU years needed • Supported by EGEE-II & BioinfoGrid european projects • Need for ressources on supercomputers (contact with DEISA) • Finally in vitro testing and structure activity relationships • Second large scale docking on EGEE in fall 2006 • Several new foreseen targets on malaria, dengue and other neglected diseases. • Resources needed: ~80 CPU years per target • Supported by EGEE-II and EELA european projects, Swiss BioGrid initiative WISDOM in EGEE-2, biomed meeting, 2006/04/28

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