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Category: Completed Research
Forum: FightAIDS@Home
Thread: FAAH Experiment 40 Updates |
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Thread Status: Active Total posts in this thread: 28
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herflick
Senior Cruncher Joined: Nov 11, 2009 Post Count: 176 Status: Offline Project Badges: 
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ABOUT THE EXPERIMENT:
----------------------------------------Experiment 40 involves screening the ChemBridge library of 1,013,483 models of compounds against the newly-discovered allosteric binding site on HIV-1 integrase. This new allosteric binding site (which we are also targeting in Experiments 38 and 39) was discovered by Professor John J. Deadman's group, and it was described in "Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design," by D.I. Rhodes, T.S. Peat, J.J. Deadman, et al., published in the journal Antiviral Chemistry and Chemotherapy, 21: 155-168 (2011). The new crystal structure from this paper that contains the atomically-detailed, 3-D data on this new allosteric site is called "3NF6.pdb". We are screening compounds against this allosteric site to try to discover new, larger, more potent allosteric inhibitors of HIV-1 integrase. It is hoped that these new allosteric inhibitors of integrase will be effective at disabling the current drug-resistant mutant superbugs of HIV integrase. For more information about this new allosteric site, see Volume 10 of the FightAIDS@Home newsletter or our recent World AIDS Day webinar (both are linked at the top of the homepage for this site). Similar to Experiment 39, in Experiment 40 we are screening one million compounds against the new allosteric site on HIV-1 integrase using two slightly different docking approaches: in the first half of these calculations, we are using the smaller dimensions of the "grid box" (the region that the compounds are allowed to explore during the docking calculations) that produced the best results in the "positive control" docking calculations that reproduced the known binding mode of this new allosteric fragment (see the figures in Volume 10 of the FAAH Newsletter, page 8). In the second half of these calculations, we are using a larger grid box, to try to find even larger allosteric inhibitors that can bind strongly with both the allosteric site and other sub-pockets that are adjacent to it. FAAH Experiment 40 involves work-units faah31,501 - faah33,528 All FAAH experimnet status information can be found at : http://fightaidsathome.scripps.edu/status [Edit 2 times, last edit by herflick at Mar 9, 2012 1:11:14 AM] |
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herflick
Senior Cruncher Joined: Nov 11, 2009 Post Count: 176 Status: Offline Project Badges:
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It's official.... Experimnet 40 is now under way !
Just got my first two work units. faah 31,502. Crunch on... ! |
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herflick
Senior Cruncher Joined: Nov 11, 2009 Post Count: 176 Status: Offline Project Badges:
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*** WEEKLY UPDATE ***
Right now WU from batch 31,596 are being sent out from Experiment 40. Based on the turnaround time time that we have averaged this week, we should be able to get to the last batch (33,528) in about 64 days, which is around May 14, 2012 . |
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herflick
Senior Cruncher Joined: Nov 11, 2009 Post Count: 176 Status: Offline Project Badges:
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*** WEEKLY UPDATE ***
Right now WU from batch 31,864 are being sent out from Experiment 40. Based on the turnaround time time that we have averaged this week, we should be able to get to the last batch (33,528) in about 43 days, which is around April 30, 2012 . |
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herflick
Senior Cruncher Joined: Nov 11, 2009 Post Count: 176 Status: Offline Project Badges:
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*** WEEKLY UPDATE ***
Right now WU from batch 32,138 are being sent out from Experiment 40. Based on the turnaround time time that we have averaged this week, we should be able to get to the last batch (33,528) in about 40 days, which is around May 4, 2012 . ***** 3 pending W.C.G. issues that will be affecting how quickly this experiment gets done are: 1. DSFL recently returned to "Normal" feeder poririty so over the next few days it will increase its share of crunching resources. 2. SN2S is currently in "Medium" feeder priority while the techs are running a Beta test to fix a few issues with SN2S. Once that issues are fixed and feeder pririty is returned to "Normal" then this project will also increase its share of crunching resources. 3. The recent server software upgrade to BOINC 700 is still balancing itself out and gradually more clients are rated for their reliability. As more clients return to zero-redundency then we will advance through work unit batches much quicker because less wingman tasks will be out there to work on. |
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herflick
Senior Cruncher Joined: Nov 11, 2009 Post Count: 176 Status: Offline Project Badges:
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*** WEEKLY UPDATE ***
Right now WU from batch 32,138 are being sent out from Experiment 40. Based on the turnaround time time that we have averaged this week, we should be able to get to the last batch (33,528) in about 40 days, which is around May 4, 2012 . ***** 3 pending W.C.G. issues that will be affecting how quickly this experiment gets done are: 1. DSFL recently returned to "Normal" feeder poririty so over the next few days it will increase its share of crunching resources. 2. SN2S is currently in "Medium" feeder priority while the techs are running a Beta test to fix a few issues with SN2S. Once that issues are fixed and feeder pririty is returned to "Normal" then this project will also increase its share of crunching resources. 3. The recent server software upgrade to BOINC 700 is still balancing itself out and gradually more clients are rated for their reliability. As more clients return to zero-redundency then we will advance through work unit batches much quicker because less wingman tasks will be out there to work on. |
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Dataman
Ace Cruncher Joined: Nov 16, 2004 Post Count: 4865 Status: Offline Project Badges: 
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Thanks for the frequent and informative updates.
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herflick
Senior Cruncher Joined: Nov 11, 2009 Post Count: 176 Status: Offline Project Badges:
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*** WEEKLY UPDATE ***
Right now WU from batch 32,393 are being sent out from Experiment 40. Based on the turnaround time time that we have averaged this week, we should be able to get to the last batch (33,528) in about 31 days, which is around May 2, 2012 . |
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Blurf
Advanced Cruncher USA Joined: Mar 19, 2007 Post Count: 118 Status: Offline Project Badges: 
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I'm back and on the case....
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herflick
Senior Cruncher Joined: Nov 11, 2009 Post Count: 176 Status: Offline Project Badges:
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*** WEEKLY UPDATE ***
Right now WU from batch 32,645 are being sent out from Experiment 40. Based on the turnaround time time that we have averaged this week, we should be able to get to the last batch (33,528) in about 25 days, which is around May 4, 2012 . ***** 2 pending W.C.G. issues that will be affecting how quickly this experiment gets done are: 1. Projects HFCC and SN2S are currently in "Medium" feeder priority. Once they return to "Normal" priority then this project will slow down a bit as the share of resources rebalances. 2. A new water project called "Computing for Sustainable Water " is set to be launched on WCG on April 16th. With a new project people rush to get batches and crunch new work units. A new project will no doubt have an effect on how quick FAAH will crunch along. |
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