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 transcript:

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

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)

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

Relaxed Complex Method

Grid Job Submission

Demo Submit docking jobs on grid Analyze results with AutoDockTools

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