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The Avian Flu Grid Project

The Avian Flu Grid Project. Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007. Outline. Meet the Team Project goals & motivation Overall scheme Running jobs on the PRAGMA grid Analyze the results w/ AutoDockTools. Meet the Avian Flu Team.

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The Avian Flu Grid Project

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  1. The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007

  2. Outline • Meet the Team • Project goals & motivation • Overall scheme • Running jobs on the PRAGMA grid • Analyze the results w/ AutoDockTools

  3. Meet the Avian Flu Team

  4. sialic acid DANA Neuraminidase as Drug Target Developed against N9 zanamivir (Relenza) Oseltamivir (Tamiflu) Clercq, Nat Rev. Drug Disc.,5: 1015-1025 (2006) Moscana, New Eng. J. Med., 353: 1363-1373 (2006)

  5. Group 1 and 2 Neuraminidases Russell et al, Nature, 443: 45-49 (2006).

  6. Relaxed Complex Method

  7. Grid Job Submission

  8. Demo • Submit docking jobs on grid • Analyze results with AutoDockTools

  9. Molecular Dynamics Simulations • Start with the crystal structure • Ligands (tamiflu), ions • Explicit solvent, 0.15M NaCl • 112,457 atoms • NAMD2, Amber99 force field • 2 fs timestep, PBC, PME • SDSC Datastar Benchmark: 112 processors, 0.21 days/ns need fast interconnect between processors - not for grid • Data: tens - hundreds of GB

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