Fold Proteins, Help Cure Diseases in Foldit Video Game
By Matt Peckham
Leave it to video gamers to find a better way to shepherd proteins into their optimal three-dimensional shapes.
Plying a freely available game and matched against automated computer routines designed to ascertain how amino acids twist into their ideal shapes, science journal Nature reports video gamers took top marks, folding proteins better than a computer.
The game, called Foldit (or Fold.it) comprises two-years of biochemistry and computer science at the University of Washington. Its goal was simple: Come up with a better, quicker way to fold proteins by harnessing the brainpower of video gamers.
“People in the scientific community have known about Foldit for a while, and everybody thought it was a great idea,” wrote UW associate computer science and engineer professor Zoran Popovic in a press statement. “But the really fundamental question in most scientists’ minds was ‘What can it produce in terms of results? Is there any evidence that it’s doing something useful?”
“I hope this paper will convince a lot of those people who were sitting on the sidelines, and the whole genre of scientific discovery games will really take off.”
Why protein folding? Because protein feeds your muscles and helps ferry signals in your brain that control your body, and because improper folding, which can produce inactive or incorrectly folded proteins, is associated with everything from allergies to several neurodegenerative diseases. Understanding how proteins ought to fold helps researchers predict and target protein structures with
Foldit, which works a bit like Tetris, asks players to actually fold a protein by shaking sidechains, wiggling backbones, and clearing locks and bands. And, it turns out, humans fare notably better than computers when crunching problems requiring risk-taking and long-term predicting–both areas necessary toward speeding protein folding.
According to Foldit’s “about” page, “The number of different ways even a small protein can fold is astronomical because there are so many degrees of freedom.”
“Figuring out which of the many, many possible structures is the best one is regarded as one of the hardest problems in biology today and current methods take a lot of money and time, even for computers. Foldit attempts to predict the structure of a protein by taking advantage of humans’ puzzle-solving intuitions and having people play competitively to fold the best proteins.”
Remember SETI@home? I used to run that app night and day on my old desktop, though less–if I’m being totally honest–to see if E.T. was phoning, than to admire how much faster my new whatever processor could pummel the University of California Berkeley’s analytic algorithms.
Passive “vanity” alien-scanning, or active protein decoding to help mitigate or actually cure neurodegenerative diseases? It’s hardly a choice for gamers, is it.
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