Biosciences Working Group Update. Wilfred W. Li, Ph.D., UCSD Karpjoo Jeong, Ph.D., Konkuk University, South Korea Habibah Wahab, Ph.D., USM, Malaysia. H5N1 Pandemic Threat. AI 2008, Bangkok, Thailand Jan 22-25, 2008 4 year Anniversary of 1 st AI outbreak.
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Wilfred W. Li, Ph.D., UCSD
Karpjoo Jeong, Ph.D., Konkuk University, South Korea
Habibah Wahab, Ph.D., USM, Malaysia
of 1st AI
source: Bankok Post; Normile, D. Science, 319:1178-9.
De Clercq, Nat Rev, 2006
Avian Flu Grid @ AFG workshop, HI, USA, August 2007
Avian Flu Grid Project @ PRAGMA 12, Bangkok, Thailand, March 2007
Funded by TATRC, NSF, and PRAGMA member institutes
Opal poster, PRAGMA 13
AFG poster, PRAGMA 13
NCI Diversity Set: 3.3 MB, 2000 compounds;
Required at each site
ZINC subset: 200,000. A few hundred MB
Docking Data: hundreds of MB
Multiple targets: HA, NA subtypes
Each target: 30~50 MD snapshots, 1~2 MB each
Simulation Data: hundreds of GB
Total data to date: ~5 TB in long term storage.
Each experiment is about 1 Petaflops accumulative in computation cost.
NA active site domain is intrinsically flexible and offers new drug design opportunities
Indonesia Karo Strain of H5N1 interaction
With avian receptor analogue LSTa
Q224L and G226S mutations modeled
Into Karo strain
Q224L and G226S mutations at HA receptor binding domain (RBD) in H5 are implicated in
host specificity switch
YoungjinChoi, Karpjoo Jeong
Cyberinfrastructure: raw resources, middleware and execution environment
NBCR Rocks Clusters
On user submit:
Invoke launchJob with right input parameters