In Foldit, gamers take on protein challenges

Almost 60,000 people around the world have played Foldit, a game much like Tetris that involves folding proteins to tackle problems in medicine such as disabling the flu virus.

Since computer scientists and biochemists at the University of Washington launched a project in 2008 that taps into the brainpower of computer gamers to fold proteins, almost 60,000 people around the world have taken on the challenge.

In the process, Foldit players have been able to best computers on problems that require radical moves, risks, and long-term vision, according to results being published on Thursday, in the journal Nature.

"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?'" says principal investigator Zoran Popovic, a UW associate professor of computer science and engineering who clearly not only loves his work, but who loved it back in his thesis days as well. "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."

In this screenshot, a Foldit player has frozen spirals to immobilize them to adjust the rest of the protein. University of Washington

There are more than 100,000 different kinds of proteins in the human body alone, forming every cell and setting the speed of chemical reactions. While scientists already know the genetic sequences of many, they're still working to understand how they fold up into complex shapes that play vital biological roles.

Thousands of computers are already calculating how physical forces would cause a protein to fold. But computers do not always outperform humans, so the UW team decided to involve the power of thousands of human brains. It turns out that in Foldit, which is free, people tend to outperform computers when a problem requires intuitive leaps or strategy shifts.

Foldit has been compared to Tetris, but instead of stacking blocks, players fold a protein. Players are awarded points based on the internal energy of the 3D protein structure, and every puzzle has a high score that players can try to best.

The Foldit energy calculations are carried out by Rosetta, which was developed by UW biochemistry professor David Baker, who co-authors the Foldit paper. Baker's group has used donated computer cycles through Rosetta@home to help sift through literally trillions of possible orientations for the chains of amino acid molecules that make up proteins.

Although the players have yet to design proteins that can, say, disable viruses or generate energy, the team at UW is confident that with so much brain and computing power involved, it is only a matter of time before medical issues are tackled. They even included in their author list an acknowledgement of more than 57,000 Foldit players--perhaps the largest to date in a scientific publication.

"We're opening eyes, in terms of how people think about human intelligence and group intelligence, and what the possibilities are when you get huge numbers of people together to solve a very hard problem," Popovic says.

The Foldit community is currently working on problems in the Critical Assessment of Techniques for Protein Structure Prediction competition. For the first time, there is a team of just Foldit players, and they are competing against the most sophisticated supercomputers in the world. Contest results will be announced in December.

A Foldit blog includes game updates, details on upcoming competitions, and special events, i.e. online chats with game developers and researchers.

 

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