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DARPA asks gamers to cure blood disease seen on battlefield

by Mike Hoffman on August 31, 2012

The Pentagon’s top tech research arm is reaching out to gaming community to help cure a blood infection that kills troops in battlefield hospitals every year.

The disease is sepsis, a blood infection that turns deadly when a patient goes into septic shock as the body tries to fight an infection. Troops often go into septic shock after suffering a massive trauma like losing a leg to a road side bomb.

Leaders of the Defense Advanced Research Projects Agency, better known as DARPA, want to fight that disease and have challenged the game and online community at Foldit, a website funded by DARPA, to help cure it. 

DARPA has asked the Foldit community to tinker with protein designs in a massive brainstorming session to design new proteins to attack the ones that cause sepsis. The hope is to design “protein-based pathogen capture reagents to be used for the removal of circulating pathogens patients’ blood as part of a larger [dialysis-like therapeutic] system,” according to DARPA.

The Pentagon had success with this approach in January when the Foldit online community of more than 240,000 gamers helped scientists remodel a reaction in organic synthesis. Had scientists had toiled over the protein design for years. Foldit users helped them solve it in three weeks.

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{ 17 comments… read them below or add one }

Pilgrimman August 31, 2012 at 12:41 pm

This is effing awesome.

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Musson August 31, 2012 at 12:53 pm

In 2011, players of Foldit helped to decipher the crystal structure of the Mason-Pfizer monkey virus (M-PMV) retroviral protease, an AIDS-causing monkey virus. While the puzzle was available to play for a period of three weeks, players produced an accurate 3D model of the enzyme in just ten days. The problem of how to configure the structure of the enzyme had stumped scientists for 15 years.

The top protien folder in the world was a woman from Manchester who was an exec assistant at a rehab clinic.

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blight_ August 31, 2012 at 3:17 pm

http://www.cs.washington.edu/homes/zoran/NSMBfold

Using a starting structure from Rosetta, a best structure was determined that matched eventual crystal structure.

What this suggests is that they went through every candidate and did additional optimizations. The fact that the 4th best was the "actual" structure is due to the fact that XRC itself requires inhibitors to lock a protein into a conformation for proper diffraction. Then there's effects of using overly high or low salt to trigger crystallization.

The other weakness is the folding funnel; that folding events commit a structure to a future series of folds, making global sampling difficult if not impossible.

"The main problem was a lack of diversity in the conformational
space explored by Foldit players because the starting models were
already minimized with the same Rosetta energy function used by
Foldit. This made it very difficult for Foldit players to get out of these
local minima, and the only way for the players to improve their Foldit
scores was to make very small changes"

and

"Thus, in a situation where one model out of several is in a near-native
conformation, Foldit players can recognize it and improve it to become
the best model. Unfortunately for the other Free Modeling targets, there
were no similarly outstanding Rosetta Server starting models, so Foldit
players simply tunneled to the nearest incorrect local minima."

Going back to the structural biology, I remain in favor of using NMR to capture conformational ensembles rather than the single PDB corresponding to a particular salt concentration and protein antagonist.

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elmondohummus August 31, 2012 at 1:44 pm

It's almost like the SETI@home project, but with actual, tangible benefits. :D

Jokes aside: It's weird to think of where crowdsourcing ends up providing a net benefit. In news reporting, you'd have thought that crowdsourced information would be awesome; national reporting with locals chipping in for flavor and details not apparent to the big picture guys. You'd have thought people would be enthusiastic about it. And there's some limited flavor of that in things like CNN's iReport offerings. But by and large, news crowdsourcing has turned into a disaster; it's either overhyped or overheated, unconfirmed stuff gleaned from Twitter, or it's idiots spamming comments sections with everything from the trivial to the stupid. It's not come anywhere near approacing its full potential.

But crowdsourcing via Foldit? If discoveries continue, it'll be a terrific success. And who'd have thunk it would be *this* that would show the benefits?

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ghostwhowalks August 31, 2012 at 6:16 pm

ITs not really 'crowdsourcing', it seems they just just their pc power as a sort of giant parallel computing project.
I dont think an individualised result would be welcomed as they would in say writing bits of computer code or contributing photos of weather stations

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blight_ August 31, 2012 at 6:27 pm

If you read the associated scientific literature, they used ab initio chemistry starting structures…which demonstrates that the real deliverable is how close the homology free prediction systems are that they only need minor tweaks by humans to get them ready for prime time.

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BlackOwl18E August 31, 2012 at 3:45 pm

And my parents said video games are a waste of time… I guess there's an exception to the rule for everything.

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blight_ August 31, 2012 at 3:55 pm

Unless you want to spend your days folding proteins from Rosetta starting structures…?

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Jack September 1, 2012 at 1:18 pm

…that saves people’s lives.

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blight_ September 4, 2012 at 9:26 am

This isn't anything particularly innovative for DARPA, as it's duplicative of work usually funded by NIH.

If DARPA wants to muscle into structural biology, perhaps the government should consider having DARPA open up structural biology grants for the academic labs already doing work in this area.

It was work by labs like David Baker's who made Rosetta, and FoldIt…and funded through NIH over a long period of time.

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KRG September 2, 2012 at 10:53 pm

Gamers spend hours upon hours trying to kill a dragon, or figure out a Portal 2 puzzle. A challenge where a gamer can see a real world benefit is another thing entirely.

Since I was young I had to figure out puzzles to beat a video game. Gamers like the challenge, and the fact it actually helps is pretty amazing. Essentially, they tap into the thousands of computers and tens of thousands of man hours that they can't with normal resources.

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Bongo September 1, 2012 at 7:01 am

Everybody knows that we, in the world of Call of Duty, have soldiers that autoheal after 5 seconds so I say this blood infection thing is BS

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Chris September 1, 2012 at 9:02 pm

Enough talk gamers. Get at it!

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morty September 2, 2012 at 10:16 pm

my random online gaming might actualy help out some day? …….. Interesting

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joe September 3, 2012 at 2:58 am

Hmm…… given the (endless) comments about China stealing innovations, here is a chance to get something back; deploy the WoW 'farmers' en masse and we'll probably have beaten AIDS, cancer and the common cold by this time sunday….

On a more serious note, briliant idea and where do I sign up?

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ghostwhowalks September 3, 2012 at 9:36 pm

$29.99 at your gaming shop !

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MONSEIUR L. September 6, 2012 at 6:06 pm

Sign me up……….yep sign me up!!!!!

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