Foldit - Design Proteins With Online Game

Foldit is an amazing effort to extend our knowledge of proteins, and possibly engineer novel protein sequences for research purposes. It is an online game that lets players design new vaccines and make enzymes for repairing DNA in diseased tissues.

Foldit is the result of a collaboration between David Baker, a leading protein researcher at the University of Washington, and Zoran Popovic, a game designer also at UW. As you can see in the video below, Foldit allows players to manipulate the long strings of amino acids that make up a protein, and design their three-dimensional structure.

(Foldit protein design game video)

Although the video of Foldit seen above has a game-like interface, the task set for the gamer is unlike that in practically any video game. "The ultimate protein configuration, and how best to get there, are not known," Popović says of Foldit.

The first levels of the game teach the game player about proteins; what does a good protein look like, and how can you manipulate your protein using the game tools. In nature, proteins are large organic compounds that serve many functions in living organisms. They are arranged in chains (as you can see in the Foldit video) joined together by peptide bonds. They spread chemical reactions, copy DNA and enable blood cells to recognize intruder viruses. Except for certain types of DNA, most other biological molecules are relatively inert elements upon which proteins act.

Scientists are just starting to be able to engineer proteins from the ground up; Baker himself recently demonstrated the first algorithm for building functional enzymes from scratch. Baker wants help in deciding what to build; Foldit generates unique designs.

Foldit game players can play alone against opponents, or as part of a team. One of the most interesting aspects of this game to me is that it pits human beings, one of nature's products, against nature itself: who (or what) can design the best proteins for specific tasks? Nature has its own way of trying millions of combinations, over long stretches of deep time. Will humans be able to do better?

The game itself won't be standing still, either; it will evolve as players use it.

Popović says that the designers will continue to improve Foldit by logging and analyzing what good and mediocre players do. "Through analyzing how people play, we're learning what the best players are doing and improving the game play with that information," he says.

Via Biologists enlist online gamers; thanks to Moira for tipping me off on this story.

Scroll down for more stories in the same category. (Story submitted 6/18/2008)

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