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Back to Section One | Back to Arts & Entertainment
posted Friday, September 23, 2011 - Volume 39 Issue 38
Gamers map structure of protease
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Gamers map structure of protease

by Mike Andrew - SGN Staff Writer

Fans of the online game Foldit have successfully modeled protease, an enzyme that retroviruses like HIV need to reproduce.

A report published by the University of Washington says the discovery 'provides new insights for the design of antiretroviral drugs.'

The journal Nature Structural & Molecular Biology published the finding on September 18.

Mapping the structure of protease is a key step toward developing new anti-viral medication therapies, but it eluded biochemists for more than a decade.

The enzyme was accurately mapped by Foldit players in less than three weeks, and opens the door to development of new antiretroviral drugs.

Foldit makes use of players' 3D puzzle-solving abilities and competitive nature to solve problems that computers alone have been unable to do.

The game was launched in 2008 as a collaboration between the University of Washington's computer science and biochemistry departments.

The university says it has two additional discoveries - one algorithmic, the other a brand-new protein - which it intends to publish in the near future.

'It's the power of citizen science,' said Firas Khatib, a postdoctoral researcher in the laboratory of UW biochemistry professor David Baker.

Baker's laboratory developed Foldit about three years ago, believing that they could tap some of the brain power that puzzle-loving humans pour into computer games.

'We wanted to see if human intuition could succeed where automated methods had failed,' Khatib explained. 'The ingenuity of game players is a formidable force that, if properly directed, can be used to solve a wide range of scientific problems.'

Foldit co-creator Seth Cooper added, 'People have spatial reasoning skills, something computers are not yet good at. Games provide a framework for bringing together the strengths of computers and humans.

'The results show that gaming, science, and computation can be combined to make advances that were not possible before.'

For the protease problem, Foldit players started with scientists' rough-draft ideas of the shape of protease based on a retrovirus that causes AIDS in monkeys.

During three weeks of play, Foldit players generated more than one million structure predictions.

The solution, reached by the winning team in only 10 days, was nearly perfect, researchers said. It gave Baker and his colleagues all the information they needed to nail down the structure almost to the last atom.

'Competitive social interaction is a very strong driving force,' Baker said.

Humans have an advantage, Khatib said, because of their intuitive ability to see the potential for a delayed payoff from moves that seem like backward steps.

'Human players can see that you may have to go down this road, not doing well for a long time, but those steps are necessary if you want to get to a more correct solution. Even the best computers and computer algorithms aren't very good at that.'

The scientists offered co-authorship to players who supplied the winning answers but all declined, asking only for recognition for their teams - Contenders Group and Void Crushers Group.

'It is a team thing. Everybody contributes,' said a player from the Contenders Group, who asked to be identified only by her Foldit username, 'mimi.'

Baker and his colleagues are posing even more difficult challenges to gamers - among them, identifying the structures of compounds that could serve important medical needs, such as inhibiting flu viruses.

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