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TheScientist | A small group of diverse individuals living on at least three continents, who call themselves The Contenders, have solved the structure of a protein that has stumped scientists for more than 10 years. And they did so from the comfort of their own homes, playing on online protein folding game called Foldit.
The Contenders’ solution and its validation were published today (September 18) in Nature Structural and Molecular Biology.
“This is the real deal,” said biophysicist Rhiju Das of Stanford University, who was not involved in the work. “I think this paper really shows how this is a new way of doing science that is more powerful than what a handful of experts could do.”
The protein in question was a retroviral protease of the Mason-Pfizer monkey virus, which causes an AIDS-like disease in monkeys. Over the last decade, many researchers had tried a variety of techniques to determine the protein’s structure, but kept coming up empty handed. “This viral protein…has really evaded the efforts of expert crystallographers and the very best automated tools,” Das said.
So one frustrated scientist, Mariusz Jaskolski of A. Mickiewicz University in Poland and the Polish Academy of Sciences, turned to an online game called Foldit. The program was designed by computation biologist David Baker of the University of Washington as an extension to his Rosetta@home program, which allows Baker to use home computers around the world to do complex calculations on protein structures. While the program ran, users would see a screen saver of the computations, Baker said, and before long, he began to get some emails about how the program wasn’t always accurate. “The protein, when it’s folding up its helix, is going left when should be going right,” users reported.
So Baker designed Foldit to allow users to alter the course of Rosetta calculations, and try to solve protein structures on their own. The goal: fold up the protein so it has the lowest energy, just as molecules tend to do in real life.
A Foldit screenshot of a protein puzzle posed to Foldit players.Center for Game Science, Department of Computer Science and Engineering, Univ. of Washington
In the past year and a half, users of the program had demonstrated their potential to solve real protein-folding problems, Baker said, so when Jaskolski came to him with this enigmatic viral protease, they decided to put the gamers to the test. Baker posed the problem to the Foldit players, and watched the responses flood in.
About 600 players from 41 teams submitted more than 1.25 million solutions. Narrowing those down to 5,000, Jaskolski and colleagues subjected them to a computational technique called molecular replacement (MR), which tests the models against X-ray crystallography data. For MR to work, the proposed structure has to be very close to accurate, in which case the MR calculations can help perfect the details. But previous attempts at MR for this protein had failed because the protein models were too far off the mark.
But The Contender’s proposed protein structure was a winner. “When we took [their] model, it was a beautiful fit to the X-ray data so we knew [they] had solved it,” Baker said. “We were just totally blown away. This is the first time that a long-standing scientific problem has been solved by Foldit players, or to my knowledge, any scientific gaming participants.”
The final breakthrough came from Foldit user mimi, a member of The Contenders and a science technician at a high school near Manchester, UK, who has been playing Foldit for about 3 years. She “tucked in a flap” of the protein that was sticking out, she explains, to make the protein more “globular.” But she emphasizes that “the achievement was very much a group effort,” noting that it wasn’t possible for her to tuck in the flap until others in the group had made their key adjustments to the protein’s structure.
“It’s kind of an unprecedented case of using computing non-specialists to solve a longstanding scientific problem,” said Alexander Wlodawer, chief of the Macromolecular Crystallography Laboratory at the National Cancer Institute.
The Contenders’ solution and its validation were published today (September 18) in Nature Structural and Molecular Biology.
“This is the real deal,” said biophysicist Rhiju Das of Stanford University, who was not involved in the work. “I think this paper really shows how this is a new way of doing science that is more powerful than what a handful of experts could do.”
The protein in question was a retroviral protease of the Mason-Pfizer monkey virus, which causes an AIDS-like disease in monkeys. Over the last decade, many researchers had tried a variety of techniques to determine the protein’s structure, but kept coming up empty handed. “This viral protein…has really evaded the efforts of expert crystallographers and the very best automated tools,” Das said.
So one frustrated scientist, Mariusz Jaskolski of A. Mickiewicz University in Poland and the Polish Academy of Sciences, turned to an online game called Foldit. The program was designed by computation biologist David Baker of the University of Washington as an extension to his Rosetta@home program, which allows Baker to use home computers around the world to do complex calculations on protein structures. While the program ran, users would see a screen saver of the computations, Baker said, and before long, he began to get some emails about how the program wasn’t always accurate. “The protein, when it’s folding up its helix, is going left when should be going right,” users reported.
So Baker designed Foldit to allow users to alter the course of Rosetta calculations, and try to solve protein structures on their own. The goal: fold up the protein so it has the lowest energy, just as molecules tend to do in real life.
A Foldit screenshot of a protein puzzle posed to Foldit players.Center for Game Science, Department of Computer Science and Engineering, Univ. of Washington
In the past year and a half, users of the program had demonstrated their potential to solve real protein-folding problems, Baker said, so when Jaskolski came to him with this enigmatic viral protease, they decided to put the gamers to the test. Baker posed the problem to the Foldit players, and watched the responses flood in.
About 600 players from 41 teams submitted more than 1.25 million solutions. Narrowing those down to 5,000, Jaskolski and colleagues subjected them to a computational technique called molecular replacement (MR), which tests the models against X-ray crystallography data. For MR to work, the proposed structure has to be very close to accurate, in which case the MR calculations can help perfect the details. But previous attempts at MR for this protein had failed because the protein models were too far off the mark.
But The Contender’s proposed protein structure was a winner. “When we took [their] model, it was a beautiful fit to the X-ray data so we knew [they] had solved it,” Baker said. “We were just totally blown away. This is the first time that a long-standing scientific problem has been solved by Foldit players, or to my knowledge, any scientific gaming participants.”
The final breakthrough came from Foldit user mimi, a member of The Contenders and a science technician at a high school near Manchester, UK, who has been playing Foldit for about 3 years. She “tucked in a flap” of the protein that was sticking out, she explains, to make the protein more “globular.” But she emphasizes that “the achievement was very much a group effort,” noting that it wasn’t possible for her to tuck in the flap until others in the group had made their key adjustments to the protein’s structure.
“It’s kind of an unprecedented case of using computing non-specialists to solve a longstanding scientific problem,” said Alexander Wlodawer, chief of the Macromolecular Crystallography Laboratory at the National Cancer Institute.
7 comments:
Yeah it's a fantasy that computers are going to take care of problem solving for us. People using computers to look at siht and play with it intelligently are a lot more powerful. Not a popular view though.
No but this could be freaking awesome. Have scientists with domain-specific knowledge design the games (a step or two beyond designing a model, granted) and then get really good, obsessed gamers to design/find the actual solutions. The gamers themselves can use computers, whatever, sure.
Freestyle chess, Vernor Vinge style (except like a lot of SF authors he seems obsessed with interface issues. Which, dudes, no, the future is now).
So, sorry for the string of comments, but you finally get your like Bobby Fischerss's (current chess champ is V. Anand of India btw) potential realized in applications. If they care to participate, which, some of the many incredibly brilliant chess masters who make like $4,000 a year or less may be available at least part-time. Someone could call them at least.
If this catches on, it's gonna put MIT undergrads out of work....,
:)
Not if they know how to program their game-obsessed peers.
program and interface..., http://www.prometheus6.org/node/28277
Nope, hadn't read about this until you posted a link.
But it makes sense. I watch some of my little cousins stay up all night just to get to the next level of a video game.
http://fold.it/
Have you tried it yet?
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