The Avian Flu Grid Project

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

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Meet the Avian Flu Team
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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)
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Group 1 and 2 Neuraminidases
Russell et al, Nature, 443 45-49 (2006).
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Relaxed Complex Method
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Grid Job Submission
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Demo

• Submit docking jobs on grid
• Analyze results with AutoDockTools

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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