ORGANIC ORIGAMI: A screen shot of a Foldit puzzle. The protein's color is based on point values and biochemical properties. The red, spiky balls indicate parts of the protein that are too close to one another, causing the player to lose points. Image: Foldit team, University of Washington
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What if the brainpower used playing video games could be channeled toward something more productive, such as helping scientists solve complex biological problems?
A team of biochemists and computer scientists from the University of Washington (U.W.) in Seattle now reports that they have successfully tapped into this human problem-solving potential. Their competitive online game "Foldit," released in 2008, enlists the help of online puzzle-solvers to help crack one of science's most intractable mysteries—how proteins fold into their complex three-dimensional forms. The "puzzles" gamers solve are 3-D representations of partially folded proteins, which players manipulate and reshape to achieve the greatest number of points. The scores are based on biochemical measures of how well the players' final structure matches the way the protein appears in nature.
When the researchers analyzed the strategies employed by a group of 57,000 Foldit players, they found that humans were better at some aspects of pattern recognition and protein structure prediction than current computational software. In fact, the gamers outperformed the computer on five out of 10 puzzles and delivered similar results on three other puzzles by using more varied approaches to solutions not used by the computer. The findings appear online August 4 in Nature (Scientific American is a part of Nature Publishing Group).
The scientists hope to incorporate the newly identified strategies into computer algorithms for improved automated determinations of protein structure. The ultimate hope is to use these techniques to design new proteins to fight diseases such as Alzheimer's and cancer as well as develop vaccines against HIV and malaria.
"This is a new and exciting approach for tackling [complex] scientific problems," says Seth Cooper, a PhD student in computer science and engineering at U.W. and lead author of the paper. "We're getting people involved, people who don't necessarily have any training in biochemistry and science. Here's a way for anyone who has a passion and interest in science to help out just by playing a video game."
Proteins are the workhorses of the body—various types of proteins are involved in nearly every cellular process, from copying genes to digesting food. They move things around in the body and serve a major structural function—comprising a major fraction of muscle and skin, for example.
In order to carry out their myriad functions proteins interact with other molecules, and these interactions are highly dependent on a protein's 3-D shape. Improperly folded proteins are at the root of many illnesses, including some cancers and cystic fibrosis as well as Alzheimer's, Parkinson's and Creutzfeldt-Jakob diseases. Therefore, to better understand what a protein does, scientists have to glean its structure.