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Web Exclusives: Structural Biology

Protein Puzzlers
By Erin Fults
Posted June 25, 2008

When you're at home, chances are you're more likely to be folding laundry than proteins.

But that's changing with new developments from the University of Washington. Rather than chasing bad guys and monsters, gamers can now spend screen time helping scientists figure out protein folding. And while the new program, Foldit, may seem like all fun and games to you, it's giving researchers insight into the structure of proteins and their roles in both diseases and treatments.

Computational biologist David Baker created the game, which is free to download, to get more people involved in the important science of protein folding. Proteins, long strings of amino acids, fold up in different shapes that determine how each protein will act. If scientists can better understand protein folding, they may be able to figure out how to treat and even prevent diseases that stem from misfolded proteins.

Baker's idea for Foldit came from his distributed computing program called Rosetta@home. This program lets Baker and his colleagues run their software on home computers whose owners "donated" the processors' downtime. As the idle machines helped solve structures, owners watched animated proteins on their screen savers. Some told Baker that they wanted to manipulate the shape and orientation of the molecules.

How to Play:

<Get a username
You could be the Codon Queen, the Genome Genius, or even Arnold Foldanator. Be creative!

<Get online
Go to External link and register as a new user. It's free!

<Get started
You're all set, now get folding!

Professor Foldit, David Baker.
Professor Foldit, David Baker.

Baker listened. With his colleagues Adrien Trehuille, Seth Cooper, and Zoran Popovic, he created Foldit to allow people to make their own moves. Within the first week of launching the program, around 30,000 people worldwide had registered and were playing.

"Distributed computing projects like Rosetta@home tap into the computing power of people around the world, but the hope is with Foldit [that] we can tap into their brain power," says Baker.

But don't worry. You don't have to know much about protein structures to play the game. In fact, Foldit's top scorer reports in his profile not knowing anything about proteins except that "you should eat [them] after exercising."

"It's not clear that knowing things about proteins actually helps you do better. It's all about the spatial relationships," says Baker.

And while little knowledge of biology and proteins is necessary to start playing, users will walk away from the game with an enhanced understanding of these structures.

"I think [Foldit] is a good way for people to learn about biomedical research, and I think that will be really neat because normally, in everyday life, you don't grapple with molecules," says Baker. "Now people have a much more vivid idea of what [proteins] are."

So how exactly does one play Foldit? It's quite simple. A protein structure will show up on your computer screen. Your job: Move it, shake it, and wiggle it into its most compact and stable form. You do this with the help of tools, such as "rubber bands" that pull pieces of the protein together and the "lock tool" that keeps a piece in place. There are also red areas along the protein that represent "clashes," which must be cleared away to obtain the correct protein structure. Beginners even get tutorials provided by a Web cartoon of Baker himself.

This 25-second clip shows a player wrangling a protein into a more compact shape. Credit: University of Washington
This 25-second clip shows a player wrangling a protein into a more compact shape. Credit: University of Washington

Currently, gamers are working with known proteins. But Baker has plans to take the game where no protein has gone before. In the fall, Foldit will offer players protein design problems that require them to develop new proteins that could disable the flu virus or break down a toxic compound, for example.

"The ones that look the best," says Baker, "we can test in the lab experimentally."

The final results could hold a key to curing diseases such as HIV, cancer, and Alzheimer's disease. Baker also hopes that the program will reach out to people in third world countries who discover an interest and talent in protein folding and decide to pursue careers in structural biology.

So how good at the game is the man behind the molecule? Baker says he's played a little but is no protein-gaming genius. He says his 13-year-old son Benjamin, who has been involved in the project since early on, is "much better at the game."

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This page last reviewed on April 22, 2011