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

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Presentation on theme: "The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007."— Presentation transcript:

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

5 Group 1 and 2 Neuraminidases Russell et al, Nature, 443: (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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