Posting in Cancer
University of Washington researchers make protein folding into a computer game. Tens of thousands of players are now unlocking the mysteries of proteins to find cures to diseases.
The rewards are higher if you play Foldit. The game taps into the compulsion that stacking blocks in Tetris does — except in this case, gamers fold proteins to predict its structure.
The rewards of winning are obvious.
Imagine if you could just go and play this game and design proteins that could be used to disarm the flu virus or treat HIV. The goal is to crack the protein folding mysteries to get us closer to new cancer treatments, biofuels, and antibiotics.
Gamers must play by the rules of physics and get points based on the internal energy of the three-dimensional protein structure.
The 3-D structures of proteins behave like biological origami. The researchers were inspired by World of Warcraft. They wanted to tap into this idea of distributed thinking by using the collective intelligence of thousands of video gamers.
You see, proteins are important for our body to function. Scientists know their 3-D structure depends on their linear amino acid sequence. But it's hard to go the other way — to begin with their amino acid sequence to figure out the structure of the proteins. That's just where the University of Washington researchers hoped this online gaming community would help.
The game was part of an experiment to see if gamers could pick up where supercomputer logic fails. Gamers can take risky moves and can consider the future, which are things computers can't do.
The study was published in Nature, thanks to the collective efforts of 57,000 Foldit players. On the Foldit blog, there has been open communication between scientists, gamers, and developers, to make sure they are on the same page.
"It's a new kind of collective intelligence, as opposed to individual intelligence, that we want to study," Zoran Popović said in a statement. "We're opening eyes in terms of how people think about human intelligence and group intelligence, and what the possibilities are when you get huge numbers of people together to solve a very hard problem.”
In 2004, University of Washington professor David Baker developed Rosetta, a program designed to predict protein structures. The program can be uploaded as a screensaver to people's home computer (so far 200,000 people have done so).
But when people asked Baker if they could help fix the proteins their computer was trying to shape, he thought it would be better to engage them with and allow them to compete with the computer.
“People saw that Rosetta was making obvious mistakes, and they were getting frustrated that they couldn’t manipulate the proteins themselves,” Baker said in a statement.
To see how humans played against computers, the researchers let the players compete directly with the computer program Rosetta. They were asked to play with ten known protein structures (that were not publicly announced yet).
Humans were good at identifying when a hydrophobic amino acid was protruding from the protein's surface and made the structural adjustments so the amino acid could be put inside. As it turns out, the people were good with remodeling the structure, but didn't perform as well when they had to start at square one.
Interestingly, Foldit's top five solo players didn't study biochemistry past high school and most of the players aren't even scientists. As long as you are good at a 3-D Tetris type of game, you are golden.
While the online game project started as a collaborative effort though Rosetta@home, the project has evolved into much more: This summer gamers have formed teams to compete in the Critical Assessment of Techniques for Protein Structure Prediction. The challenge is to design a new protein.
John Bohannon previously wrote in Wired:
Baker doesn't want to lose Foldit's momentum. He and Popović have given the players a challenge: Design a new protein. Baker's lab is developing targets for cancer, AIDS, and Alzheimer's, and the folders' task is to build a small protein drug with the right shape and binding properties. This isn't just an intellectual exercise. Baker says he will synthesize the most promising structures and test them in his lab. These proteins could actually have therapeutic value in the real world, outside the game. And if they do, the Foldit players will share the credit. It might be the first time that a computer game's high score is a Nobel Prize.
The whole idea of using games to solve scientific problems is relatively new. But I wouldn't be surprised to see more of them in the future.
"I hope this paper will convince a lot of those people who were sitting on the sidelines, and the whole genre of scientific discovery games will really take off," Popović said in a statement.
In America, that amounts to 250 million people playing games on average 10.5 hours a week. So if you're already playing video games, you might as well put your brain power to good use.
Forget Tetris. Now go fold those proteins.
Aug 5, 2010