Folding@Home Exascale Supercomputer Finds Potential Targets For COVID-19 Cure (networkworld.com) 38
An anonymous reader quotes a report from Network World: The Folding@home project has shared new results of its efforts to simulate proteins from the SARS-CoV-2 virus to better understand how they function and how to stop them. Folding@home is a distributed computing effort that uses small clients to run simulations for biomedical research when users' PCs are idle. The clients operate independently of each other to perform their own unique simulation and send in the results to the F@h servers. In its SARS-CoV-2 simulations, F@h first targeted the spike, the cone-shaped appendages on the surface of the virus consisting of three proteins. The spike must open to attach itself to a human cell to infiltrate and replicate. F@h's mission was to simulate this opening process to gain unique insight into what the open state looks like and find a way to inhibit the connection between the spike and human cells.
And it did so. In a newly published paper, the Folding@home team said it was able to simulate an "unprecedented" 0.1 seconds of the viral proteome. They captured dramatic opening of the spike complex, as well as shape-shifting in other proteins that revealed more than 50 "cryptic" pockets that expand targeting options for the design of antivirals. [...] The model derived from the F@h simulations shows that the spike opens up and exposes buried surfaces. These surfaces are necessary for infecting a human cell and can also be targeted with antibodies or antivirals that bind to the surface to neutralize the virus and prevent it from infecting someone. "And the tech sector played a big role in helping the find," adds the anonymous Slashdot reader. "Microsoft, Nvidia, AMD, Intel, AWS, Oracle, and Cisco all helped with hardware and cloud services. Pure Storage donated a one petabyte all-flash storage array. Linus Tech Tips, a hobbyist YouTube channel for home system builders with 12 million followers, set up a 100TB server to take the load off."
And it did so. In a newly published paper, the Folding@home team said it was able to simulate an "unprecedented" 0.1 seconds of the viral proteome. They captured dramatic opening of the spike complex, as well as shape-shifting in other proteins that revealed more than 50 "cryptic" pockets that expand targeting options for the design of antivirals. [...] The model derived from the F@h simulations shows that the spike opens up and exposes buried surfaces. These surfaces are necessary for infecting a human cell and can also be targeted with antibodies or antivirals that bind to the surface to neutralize the virus and prevent it from infecting someone. "And the tech sector played a big role in helping the find," adds the anonymous Slashdot reader. "Microsoft, Nvidia, AMD, Intel, AWS, Oracle, and Cisco all helped with hardware and cloud services. Pure Storage donated a one petabyte all-flash storage array. Linus Tech Tips, a hobbyist YouTube channel for home system builders with 12 million followers, set up a 100TB server to take the load off."
Thanks Slashdot (Score:5, Funny)
I told my wife that I'd like to try Folding@home. She dropped a big tub of laundry in front of me.
Re: Thanks Slashdot (Score:5, Funny)
Re: Thanks Slashdot (Score:1)
Plaid out.
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I told my wife that I'd like to try Folding@home. She dropped a big tub of laundry in front of me.
Still better than Folding@Shoney's. Jerry could only manage six folds [youtube.com] but, to be fair, that was in a Series 9000.
Comment removed (Score:4, Informative)
Re:You can help, there is still work to be done! (Score:4, Interesting)
Processors do not as a rule run cranked at full tilt and 'waste cycles' that you could otherwise contribute. I haven't run the math, but I'm pretty sure it is energy inefficient to the point you'd do more good by just giving a dollar a day to whatever lifesaving organization you prefer. Preferably one that won't abuse your good will and flood your goddamn rl mailbox with goddamn solicitations.
I suppose if you are already using electric heating in the home it would be a good value in that situation.
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I suppose if you are already using electric heating in the home it would be a good value in that situation.
Bingo. I have electric heating at home, and I turned F@H back on now that the weather is cooler. I doesn't cost me anything to contribute since I would be paying for the heat one way or another.
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Depending on your climate, you might be better served investing in a different heating system. If your winter nights mostly average above freezing, a heat pump will be much more efficient than resistive electric heating. If they're colder, a furnace of some sort will probably be more cost-effective. When my house's furnace died years ago, I replaced it with a hybrid heat pump/furnace, and the savings compared to the furnace-only unit have been considerable.
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Or if the temps regularly get below freezing, a ground ("geothermal" ... which it isn't, it's indirect solar thermal) heat pump.
Even just a gas furnace is probably more cost effective than resistive heating, though.
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At least in my area, installing a geothermal system requires about $40,000 worth of trench digging and pipes laid in one's yard, which doesn't really ever break even. It might be more affordable on new construction, but when I was replacing my furnace, the only system that was obviously less cost-effective than geothermal was burning paper money for heat.
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Yes, you generally either have to do it during initial construction, or you have to have a friend with a backhoe. Or an army of undocumented immigrants with shovels, but they're harder to come by these days.
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Zimbabwe dollars will work.
If there is too much solar or wind generated energy instead of costly storage or curtailment just turn on a million computers. Use the heat to make dried fruit of jerky.
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Natural gas is ridiculously cheap in general. It seems like they can't give it away. Something like 50% of it is flared off at the well (at least in the Permian Basin wells)... burned and released into the atmosphere without even an attempt to bottle and sell it. Not enough volume is selling to warrant constructing a shitload of storage space, which would end up storing years' worth of consumption. It's treated like a byproduct they have to dispose of, it just happens to come out of the well along with the
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How old of computers can be use? Can I use my old PowerBook G4 1 Ghz, Pentium 1 MMX 150 Mhz, dual core AMD Athlon 64, 15" 2008 MBP, etc.?
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For many if not most people, there is no good reason not to run this.
Perhaps because my electric bill is already way too high?
Take any plug-in power meter like a Kill-A-Watt and run your PC through it, and measure the difference between idle and running something very CPU / GPU intensive like Folding @ Home. You'll be shocked at the result, and leaving your machine 24 hours a day running work units is a great way to drive up your electric bill.
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If you can't afford to contribute to this worthwhile effort, then you shouldn't.
If you can, then it's a great cause. They've done a lot of great research over the years.
Impressive! (Score:5, Interesting)
the Folding@home team said it was able to simulate an "unprecedented" 0.1 seconds of the viral proteome
Considering that protein folding usually takes between microseconds and milliseconds, that's a REALLY long sequence!
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It's my understanding that molecules move at the speed of a few femtoseconds (10**-15). If that's correct, the 0.1 seconds represents something on the order of 100 Trillion "frames" of molecular movement.
Very impressive. But a very slow movie to watch.
Next step (Score:2)
OK now use Autodock Vina to run molecules in the ZINC15 database against those targets to see which will bind.
It's personal (Score:4, Interesting)
I have been part of Folding@Home (F@H) for several years, and focused my F@H client on SARS-CoV-2 exclusively as work units ramped up. I have always been proud to be a tiny part of F@H, committing increasingly capable GPUs to the fight.
I lost my mother to Covid-19 in the first week of October. Keep up the good fight F@H.
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That's great, everybody pitches in (Score:1)
Now the question is: which pharmaceutical company will use the data from all that good will and reap obscene benefits for themselves alone?
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The question whether these companies will lower their prices because they got this research for free, or if they will keep the money saved to increase their profit margins, is left as an exercise for the reader.
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You need to get it to market and there are still expensive trials, even with "warp speed" super-fast track.
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I believe that Richard Stallman hated passwords. If want to piss a farmer off, lock the doors to his house. He may need to break a window to get into his house. Shotguns, dogs, goats and bulls are better deterrents than a lock.
Locks can be a pain, someone locks your cmos or encrypts your drive. TPM can go to HE??
Distributed research, distributed benefit (Score:2)
Now the question is: which pharmaceutical company will use the data from all that good will and reap obscene benefits for themselves alone?
It's impossible for a company to reap benefits for "themselves alone". To make money, a company needs to sell stuff to people. Transactions benefit both the buyer and the seller. If a buyer wouldn't benefit from the transaction, they just won't buy, leaving no benefit for the company. The sale of a drug benefits the buyer (through the beneficial effect of the drug) and the seller (through cash profit). And if a drug keeps someone out of the hospital, other people -- those who need hospital resources -- bene
Only ? (Score:1)
Re: Only ? (Score:2)
Yes, but it's 100TB of science vs your 100TB of "science".
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Both are detailed biological study information.
Skeptical (Score:2)
Other receptors ... (Score:2)
The following is from research papers that were published in the past few weeks.
In addition to ACE2, there are other receptors that either facilitate entry into cells (making the virus more infectious) or increase its pathogenicity (causing more severe symptoms).
The other receptor that helps entry is neuropilin-1 [wikipedia.org] , which is more abundant in the upper respiratory tract. That may explain the the first phase of infection and spread while asymptomatic or having mild symptoms. Finding a way to block that recept