Posted on 08/15/2009 8:41:55 AM PDT by texas booster
SUMMARY. The influenza virus infects people and animals by binding to complex sugar molecules on the surface of the respiratory tract. Bird viruses bind most strongly to bird cell-surface sugars and human viruses bind most strongly to human cell-surface sugars. As the recent swine-origin influenza virus has demonstrated, there is considerable overlap between the binding ability of human and pig viruses to cells of the other host. Changes to this binding affinity are one key component for viruses to make a jump between species, and it is difficult to predict the necessary mutations ahead of time. We would like to predict high-risk mutations to enable better surveillance and early control of potential inter-species transmission events. This work represents a first step in that direction, as we examine mutations to H5N1 avian influenza that alter sugar binding. We use Folding@Home as a powerful computational screen to evaluate mutations that will eventually require experimental testing to verify.
ABSTRACT. Influenza virus attaches to and infects target cells via binding of cell-surface glycans by the viral hemagglutinin. This binding specificity is considered a major reason why avian influenza is typically poorly transmitted between humans, while swine influenza is better transmitted due to glycan similarity between the human and swine upper respiratory tract. Predicting mutations that control glycan binding is thus important to continued surveillance against new pandemic influenza strains. We have designed a molecular-dynamics approach for scoring potential mutants with predictive power for both receptor-binding-domain and allosteric mutations similar to those identified from clinical isolates of avian influenza. We have performed thousands of simulations of 17 different hemagglutinin mutants totaling >1 ms in length and employ a Bayesian model to rank mutations that disrupt the stability of the hemagglutinin−ligand complex. Based on our simulations, we predict a significantly increased koff for seven of these mutants. This means of using molecular dynamics analysis to make experimentally verifiable predictions offers a potentially general method to identify ligand-binding mutants, particularly allosteric ones. Our analysis of ligand dissociation provides a means to evaluate mutants prior to experimental mutagenesis and testing and constitutes an important step toward understanding the determinants of ligand binding by H5N1 influenza.
Combining Molecular Dynamics with Bayesian Analysis...
A brief summary and technical abstract follow. This work incorporates results from projects 2668-2675. Those projects are also continuing to generate useful data for further analysis. Thank you for your contribution to science!
How does it work?: You download a safe, tested program (see link below) that is certified by Stanford University. It gets work from Stanford, runs calculations using your spare computer power, and sends the results back to the University.
Is it safe? Yes! Folding@Home rarely effects computer performance in any way and won't compromise your privacy in any way. It only uses the computing power you aren't using so it doesn't slow down other programs.
How do I get started folding for Team FreeRepublic?:
1.) Download the folding program from Stanford University's folding download page (Folding@home Client Download). Type in your desired user-name.
2.) Type in 36120 for the team number. THIS IS VERY IMPORTANT - if you get the number wrong, you won't be folding for team FreeRepublic!
3.) The third question asks, "Launch automatically at machine startup, installing this as a service?" - We recommend you answer YES. Otherwise you will have to manually start the program after every reboot.
How can my computer help? Even if they were given exclusive access to all of the world's supercomputers, Stanford still wouldn't have as much processing power as they get from the supercluster of people's desktop systems Folding@home relies on. Modern supercomputers are essentially a cluster of hundreds of processors linked by fast networking. But Stanford needed the power of hundreds of thousands of processors, not just hundreds.
There's no reason to not get involved! It's free, easy, and you can know you're helping every minute without lifting a finger.
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List of Relevant Folding Links
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Competition (Not!!) Dummies ..Daily Kos
Dummie Folding Threads #7 #8 #9#10#11 #12
Hey DUmmies, can't ya'll post a new thread at least once a year?
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Other Useful Stuff - Links
How much are those work units worth? And what are they?
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BTTT
A shout out to those folders to let you know that your folding efforts have proven, published results.
Please check your systems and ensure that they are still plugging away finishing new research.
I'm still here... but with fewer systems on-line than before. Thanks for the update.
I found a few systems still running the older F@H console for Window 5.03/5.04. If you find this version, please upgrade to the new 6.23 and enjoy a 20% speed improvement.
Woohoo!
Congrats on the 5,000,000 mark.....C
Congrats on 1,000,000 points!!!!
later
Congrats on the milestones. Our team also reached 100 million points this past week.
Look for me to move up on the weekly points if this new machine will fold!
THe 9600GSO is a very nice card. I looked long and hard at the EVGA version before I went with a GTS250. Make sure you get lots of fans on the box.....C
I believe the 9600GSO is the same card as the 8800GSO, and should have the same PPD. Nvidia just renamed it so they could keep selling it along with their other 9xxx cards. I have two 8800GS cards, somewhat overclocked, and they get about 3500 PPD each. They’re really nice cards. I use the EVGA Precision software to overclock the cards and set the fan speed to 100%, but they’ll also run relatively cool at default clock and fan speeds.
I don’t do any CPU folding, but I’m guessing the SMP client running on your quad proc should be good for another 2-3K PPD. That will be a nice bump.
3000 ppd for the 9600GSO and 2000 ppd for the SMP.
Not bad for a machine I have $800 in including the 23" monitor, the 9600GSO and a new 500 watt power supply. That (with my current machines)should get me near 60k points/week.
I suppose the kids can do some homework and gaming on it too...
Have you (or anyone who might see this) heard of any issues connecting to the Work Server? My FAH client has been trying to submit results most of the day, and has not been able to get ack of results, or get new work.
Will check the forums after work.
Thanks for responding. Good to know it’s not something on my end. Must be having server issues.
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