October 1, 2008 Computer scientists designed a computer game based on the principles of biochemistry. It allows amateurs to compete against and collaborate with specialists to design protein structures. Introductory levels teach the general governing concepts that users must understand before moving on to design complicated, potentially useful molecules.
What if instead of waging war or dropping blocks, gamers set their sights on something like a new HIV vaccine? Sounds strange, but biochemistry might be the new must-play video game.
It looks and sounds like a computer game, but Foldit is much more than just a computer game -- it's crucial biochemistry research.
Biochemist David Baker wants to discover the unique folding of proteins to better understand how they make our bodies work. A friend suggested turning this scientific puzzle into a game. That's where computer scientist Zoran Popovic and his team come in.
"You no longer need to get a degree in biochemistry to actually start doing this stuff," says Zoran Popovic, Ph.D., an associate professor in the department of Computer Science and Engineering at the University of Washington in Seattle.
The game's introductory levels "trick" you into learning all the concepts you need to know. Then all you do is play -- alone or in teams.
"I know that some of our users have kind of described it as Tetris on steroids or something," Dr. Popovic says. The goal is to get the highest score by folding the proteins based on the same criteria they use in the lab. Each protein is a puzzle -- the more people play, the better chance a correct "fold" will be discovered for each protein. Eventually the puzzles could be used to help make vaccines and even cure genetic diseases.
"You can get into work and say I stayed up all night -- [but] I wasn't playing Halo," says David Baker, Ph.D., a biochemist at the University of Washington in Seattle. "I was designing an HIV vaccine."
ABOUT COMPUTER MODELING: Computer modeling is used to represent the structure and appearance of both static objects, such as building architecture, and dynamic situations, such as a football game. With Foldit, game players have the opportunity to use a computer model to test the benefits of changing the structure of a protein. Foldit and other computer models can provide cutaway views that let users examine aspects of an object that are invisible even to the most powerful microscopes, as well as visualization tools that can provide many different perspectives. Computer models enable users to run companies and civilizations, fight battles, and play football games.
COMPLICATED MOLECULES: Polymers are large molecules made up of long repeating chemical units joined together in a chain, like beads on a string. Biological polymers are among the largest and most diverse molecules in the natural world, often containing billions of atoms. Human DNA is a polymer that can be thought of as billions of beads on a string. Proteins are polymers made up of 20 different amino acids, and the solid plastics used in a broad range of consumer products are polymers made of various types of "monomers" or smaller molecules. When monomers link together to form a polymer, this process is called polymerization, but they don't always link together in straight chains of regularly repeating monomers. Secondary molecules called catalysts can coax monomers to link together in certain configurations, and also speed up reaction times. This is how most synthetic polymers are created.
The American Association of Pharmaceutical Scientists contributed to this report. This report has also been produced thanks to a generous grant from the Camille and Henry Dreyfus Foundation, Inc.