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Protein-Folding Game Taps Power of Worldwide Audience to Solve Difficult Puzzles

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A cooperative online game that puts volunteer “gamers” to work folding proteins has attracted 50,000 players whose “distributed thinking” has, in some cases, proven more powerful than computers in predicting the three-dimensional structure of proteins. Extension of these efforts could one day pay off in the design of new proteins that help fight disease, sequester carbon, or clean up the environment.

The free game, called Foldit, is the brainchild of David Baker, a Howard Hughes Medical Institute biologist, and colleagues Zoran Popovic and Seth Cooper, who are in the computer science department at the University of Washington. The online community of Foldit players is now helping the researchers as they attempt to crack “the protein-folding problem,” one of molecular biology’s toughest challenges.

“There's a lot of creativity and energy out there that is being spent on computer games that could go into solving scientific problems.” said David Baker.

“The positive response to Foldit makes me very optimistic for getting the general public involved in science,” says Baker. I’m very pleased we’ve been able to harness some of that energy.”

In creating Foldit, the researchers partly drew inspiration from “World of Warcraft” and other online games that have attracted millions of players who compete and cooperate to solve puzzles. Baker calls Foldit a success in “distributed thinking” – presenting scientific problems to the masses and attracting a talented crowd that contributes new solutions. An article describing Foldit is published in the August 5, 2010 issue of the journal Nature.

With programming and game design provided by University of Washington computer scientists Seth Cooper, Adrien Treuille and Zoran Popovic along with Firas Khatib and other researchers in Baker’s group, Foldit debuted in May 2008 as an interactive extension of Rosetta, a computer program Baker developed to predict protein structures.

Solving protein structures is one of the preeminent challenges in biology, requiring labor-intensive x-ray crystallography to divine the arrangement of the thousands of atoms that comprise each protein. Rosetta, in contrast, relies on a large scale search for the lowest energy shape of each protein – a computer-hungry process that requires trillions of calculations. Baker quickly realized that Rosetta was limited by the amount of supercomputer time he could secure. So in 2004 he developed a distributed version of Rosetta that individuals could load on their home or office computers to help perform some of Rosetta’s calculations.

“Designing new proteins to fit a desired shape is something that Foldit players should be very good at,” says Baker. While it may be years before a new crowd-sourced virtual protein helps solves a real-world problem, Baker is convinced that day will arrive. “The moment we test a protein design in the lab that came from one of the Foldit players and find it carries out the desired new function will be an amazing day for science,” he says.