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How online gamers helped UW researchers solve AIDS mystery

Greg Lamm on Saturday, September 17, 2011

University of Washington researchers have teamed up with gamers to make a breakthrough in AIDS research that could unlock new drug treatments.

The game at the center of the breakthrough is Foldit, an online game that lets players collaborate and compete in predicting the structure of protein molecules. Playing Foldit, gamers helped researchers solve a problem that has stumped them for more than a decade: How to configurate the structure of a retrovirus enzyme related to AIDS.

UW researchers say this is the first time they are aware that researchers have tapped into the expertise of games to solver a long-standing scientific problem.

While the problem had befuddled researchers for years, it took gamers only a few days to solve it. The results suggest that humans and computer models can learn from each other in real-time.

“People have spatial reasoning skills, something computers are not yet good at,” said Seth Cooper, of the UW Department of Computing Science and Engineering, who is a co-creator of Foldit. “Games provide a framework for bringing together the strengths of computers and humans. The results in this week’s paper show that gaming, science and computation can be combined to make advances that were not possible before.”

Solving the structure of the retrovirus enzyme is a big leap forward, said researchers, because the enzyme is in a class called retroviral proteases that plays a critical role in how the AIDS virus matures and multiplies. Now that researchers know what the enzyme looks like, there is hope that it will speed up the development of anti-AIDS drubs that can block the enzymes.

“These features provide exciting opportunities for the design of retroviral drugs, including AIDS drugs,” wrote the authors of a paper appearing Sunday in Nature Structural & Molecular Biology.

Reseachers say figuring out the virus enzyme structure, “indicates the power of online computer games to channel human intuition and three-dimensional pattern matching skills to solve challenging scientific problems.”

And researchers have gamers — who are listed as co-authors of the paper — to thank for their breakthrough.

“We wanted to see if human intuition could succeed where automated methods had failed,” Firas Khatib of the University of Washington Department of Biochemistry, said in a statement. Khatib is a researcher in the protein structure lab of UW biochemistry researcher David Baker.

Fold-it was created by computer scientists at the University of Washington Center for Game Science, working with the Baker Laboratory.

“The focus of the UW Center for Game Sciences,” Zoran Popovic, associate professor of computer science and engineering, said in a statement. “Is to solve hard problems in science and education that currently cannot be solved by either people or computers alone.”

UW says the the online protein folding game drew in thousands of avid players from around the world:

They taps into their 3-D spatial abilities to rotate chains of amino acids in cyberspace. New players start at the basic level, “One Small Clash,” proceed to “Swing it Around” and step ahead until reaching “Rubber Band Reversal.”

Direct manipulation tools, as well as assistance from a computer program called Rosetta, encourage participants to configure graphics into a workable protein model. Teams send in their answers, and UW researchers constantly improve the design of the game and its puzzles by analyzing the players’ problem-solving strategies.

Figuring out the shape and misshape of proteins contributes to research on causes of and cures for cancer, Alzheimer’s, immune deficiencies and a host of other disorders, as well as to environmental work on biofuels.

Games like Foldit are evolving. To piece together the retrovirus enzyme structure, Cooper said, gamers used a new Alignment Tool for the first time to copy parts of know molecules and test their fit in an incomplete model.

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