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Former Member
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Many thanks - Phase 1 now completed!

It's official - “Influenza Antiviral Drug Search - Phase 1” is done!

Similar to our related “Discovering Dengue Drugs-Together” project, all Phase 1 results that you have generated to help find new influenza antivirals are on our disk servers. They are being processed and double-checked. Thank you for your efforts and help!

Phase 1 is only the first step on our path to discovering new influenza drugs. Phase 1 has systematically tested ~3 million small "drug-like" molecules against 9 influenza neuraminidase strains (including Tamiflu-resistant and Relenza-resistant strains). These 27 million individual docking experiments were completed in ~5 months. Our 30-node high-performance cluster would have needed to run nonstop for 100 years to finish these calculations.

Phase 1 identified numerous that could potentially interact with each neuraminadase target. Typically, ~90-95% of Phase 1 “hits” turn out to be false positives when tested in the laboratory. Thus, Phase 1 hits are very inefficient to pursue with laboratory testing.

“Influenza Antiviral Drug Search - Phase 2” is designed to reduce the number of Phase 1 false positives. In Phase 2, we will complete ~2000 computationally demanding free energy calculations for each protein target (each calculation uses a promising Phase 1 hit)s. These calculations will eliminate many of the Phase 1 false positives and produce refined hit lists that are expected to contain ~80% true positives. Testing Phase 2 hits in the laboratory will be much more productive, efficient, and rewarding than testing Phase 1 hits.

Beta testing is underway for “Discovering Dengue Drugs – Phase 2”. The programs and workflow required for ”Influenza Antiviral Drug Search - Phase 2” are similar to the dengue project. Thus, “Influenza Drug Search - Phase 2” should launch soon after “Discovering Dengue Drugs - Phase 2” starts.

We look forward to your continued help and generosity as we work together to find new cures for influenza infections.

All my best, and many thanks!

Stan

P.S. Although completed, IADS-1 will remain officially active on the grid. From time to time, we will need to test additional drug targets to help refine our evolving drug predictions, so do not be surprised if new IADS-1 workunits occasionally show up in your cache.
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[Edit 2 times, last edit by Former Member at Nov 4, 2009 9:23:45 PM]
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Former Member
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Re: Many thanks - Phase 1 now completed!

My / our thanks to you , a privilege to make a contribution for your research biggrin




Thanks again for the update and best of luck smile


JP
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falconet
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Re: Many thanks - Phase 1 now completed!

Thanks for the update!!
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damir1978
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Re: Many thanks - Phase 1 now completed!

Thank you VERY MUCH for the update !
We really appreciate ANY REAL information regarding the projects we are all involved in.
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Randzo
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Re: Many thanks - Phase 1 now completed!

Thanks a lot we are looking forward to phase 2 of this projetcs.
Please keep us informed. We highly appreciate any news.
Good luck.
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Former Member
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Re: Many thanks - Phase 1 now completed!

“Influenza Antiviral Drug Search - Phase 2” is designed to reduce the number of Phase 1 false positives. In Phase 2, we will complete ~2000 computationally demanding free energy calculations for each protein target (each calculation uses a promising Phase 1 hit)s. These calculations will eliminate many of the Phase 1 false positives and produce refined hit lists that are expected to contain ~80% true positives. Testing Phase 2 hits in the laboratory will be much more productive, efficient, and rewarding than testing Phase 1 hits.

Hi Stan,

Can you estimate the total number of WU that will be processed and the number of months needed to calculate those WU, based on the average daily WU crunched for Phase 1?
[Nov 5, 2009 4:17:36 AM]   Link   Report threatening or abusive post: please login first  Go to top 
bieberj
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Re: Many thanks - Phase 1 now completed!

Thanks for the great news Stan. We will be waiting for Phase II - both for dengue drugs and AIDs.
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Former Member
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Re: Many thanks - Phase 1 now completed!

Can you estimate the total number of WU that will be processed and the number of months needed to calculate those WU, based on the average daily WU crunched for Phase 1?


Here are my preliminary estimates that should hold for either project. These estimates may be on the optimistic side, and will likely change when we finish beta testing.

WCG CPU time: 41 days/ligand x 2000 ligands/target x 10 targets x 2 (redundancy) so ~4500 WCG CPU yrs

Wall time: assuming 30 WCG CPU yrs/day gives ~150 days to complete Phase 2

Workunits: 200 WU/ligand x 2000 ligands/target x 10 targets x 2 (redundancy) so ~8,000,000 WU

I hope my math skills are intact this morning....

Time for coffee coffee coffee coffee

Stan
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[Edit 3 times, last edit by Former Member at Nov 6, 2009 2:43:58 PM]
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smeyer55
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Re: Many thanks - Phase 1 now completed!

Wall time: assuming 30 WCG CPU yrs/day gives ~150 days to complete Phase 2

Wow, that will be a fast project. I'll have to focus on that to get a Sapphire badge.
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Re: Many thanks - Phase 1 now completed!

Thanks Stan
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