The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 -...
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![Page 1: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062511/55149be955034640138b46b2/html5/thumbnails/1.jpg)
The Avian Flu Grid Project
Rommie Amaro & Dong Xu
University of California, San Diego
PRAGMA 13 - NCSA
Sept 25, 2007
![Page 2: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062511/55149be955034640138b46b2/html5/thumbnails/2.jpg)
Outline
• Meet the Team• Project goals & motivation• Overall scheme• Running jobs on the PRAGMA grid• Analyze the results w/ AutoDockTools
![Page 3: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062511/55149be955034640138b46b2/html5/thumbnails/3.jpg)
Meet the Avian Flu Team
![Page 4: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062511/55149be955034640138b46b2/html5/thumbnails/4.jpg)
Neuraminidase as Drug Target
Developed against N9
sialic acid DANA 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
![Page 7: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062511/55149be955034640138b46b2/html5/thumbnails/7.jpg)
Cluster
Cluster
Cluster
Autodock
NAMDOther
Resource
12 CPUs
Autodock
BLAST
Other Resource
64 CPUs
NAMD
Autodock 8 CPUs
Other Resource
CSF4 Meta-Scheduler
Available Resource Lists
Resource
Scheduling Modules
Resource Requirements
Autodock1990 CPUs
NAMD24 CPUs
Autodock100 CPUs
Autodock1 CPU
ˇˇ
ˇˇ
User
Grid Job Submission
![Page 8: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062511/55149be955034640138b46b2/html5/thumbnails/8.jpg)
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