Sunday, May 11, 2008

Instead of pitting players against monsters, criminals or aliens, a new computer game enlists them in the real-life fight against other deadly enemies: diseases and viruses.

Gamers who play “Foldit,” a computer game developed by University of Washington scientists, will actually be protein folding, a process used to unlock the mysteries of human proteins, which help the body perform countless functions, from breaking down food to carrying oxygen in the blood, but also play roles in some diseases and viruses.

“We’re hopefully going to change the way science is done, and who it’s done by,” said Zoran Popovic, an associate professor of computer science and engineering who was part of the team that developed the game. “Our ultimate goal is to have ordinary people play the game and eventually be candidates for winning the Nobel Prize.”

Scientists spend countless hours and dollars trying to better understand the shape and function of proteins, and the creators of “Foldit” hope the game will transform game players into armchair scientists who will help make discoveries about biological mysteries, ranging from Alzheimer’s disease to vaccines.

“We’re trying to use the brain power of people all around the world to advance biomedical research,” said team member David Baker, a professor of biochemistry and a Howard Hughes Medical Institute investigator.

Each protein is made up of an amino acid chain that folds into a particular ideal shape, emitting the lowest amount of energy. The scientific community already knows the genetic makeup of many proteins, but doesn’t know how they fold up into these complex shapes.

“Foldit” turns protein folding into a competitive sport, as players click and twist the snakelike 3-D images on their screen. The goal is to condense the protein down to its most compact shape, with the fewest number of gaps or holes. The “Foldit” computer program calculates a score, and high scores are investigated further by the University of Washington scientists.

Finding the ideal structure and shape of a protein “can help you understand what the protein does, how it acts, and might provide a starting point to block its action if it’s involved in disease,” Mr. Baker said.

Initially, as “Foldit” was tested, about 700 players were given proteins whose ideal structure and shape were already known.

Last week, the game was opened to the public and included proteins with unknown shapes. The University of Washington team presented the game at a gaming conference in Baltimore on Thursday, and now about 30,000 people have played the game, which is available on the Internet at “”

The team plans to track and record what the best players are doing and refine the game accordingly, Mr. Popovic said.

In the next version of “Foldit,” planned for a summer release, players will be able to design brand new proteins aimed at neutralizing toxic waste or fighting HIV, Mr. Baker said.

For instance, he said, players could be presented with the virus that causes the common cold, along with a protein that scientists think shows some promise of being able to combat it. Like scientists, players would be able to alter the protein’s makeup, add or subtract amino acids, and change its shape to make it fit tightly into the flu virus, like a jigsaw puzzle piece that could theoretically deactivate the virus.

Ben Sawyer, co-founder of the Games in Health Project, said scientists and gamers are constantly finding new and exciting ways of merging their two fields to promote health research.

During the two-day Baltimore conference, his group heard from an epidemiologist who was able to glean important public health information by studying what happened in the virtual world after a popular video game released a blood disease into the game.

Games are also being used to motivate people who are in physical therapy, Mr. Sawyer said.

In the world of protein-folding, Sony, Intel and others teamed up with Stanford University to develop a program that uses computers to try to fold proteins. Mr. Baker developed a similar computer program in 2005.

But “Foldit” takes all of this one step further by harnessing the brain power of potentially thousands of people to help solve these protein puzzles, Mr. Sawyer said.

“I think it’s well-designed,” he said of the new game.

The game was developed by doctoral student Seth Cooper and postdoctoral researcher Adrien Treuille, both in computer science and engineering. They worked with Mr. Popovic and Mr. Baker, along with David Salesin, a professor of computer science.

University of Washington team members said some people simply seem to be gifted at solving 3-D puzzles like the protein shapes — and some are much more capable than scientists. Mr. Popovic said that in the initial group of 700 players, a few stood out with high scores immediately, including one person from New Zealand and another from Canada.

Mr. Baker said his 13-year-old son, Benjamin, is faster at folding proteins than he is.

He added, “I imagine that there’s a 12-year-old in Indonesia who can see all this in their head.”

The “Foldit” project was funded by the Defense Advanced Research Projects Agency, the Howard Hughes Medical Institute, Microsoft and Adobe Systems, and through fellowships at Nvidia and Intel.

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