Protein folding is among the most complex problems for scientists to figure out. Calculating the countless atomic interactions that determine a given protein’s 3-D shape is a huge task. It’s also arguably among the most important: proteins of thousands of different types allow living things to complete all sorts of functions, and each of these functions depends not only upon the chemistry of the chain but also upon its precise shape. In order to do their job, proteins must be made of the right stuff and organized in the right way. That means that completely understanding processes from digestion to cell formation to immune responses and more hinges on understanding protein folding. And if scientists can learn more about the patterns of protein folding, it may help them to design new proteins that can help combat a number of diseases. So who should we turn to to solve these difficult and fundamental puzzles? If you ask biochemist David Baker of the University of Washington, you may get an answer you wouldn’t expect: Gamers.
The idea began with a contest, the Community-Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP), in which teams compete to predict the shapes proteins will take based on the sequence of their parts. The contest encourages scientists to come up with new approaches for figuring out how proteins take the shapes they do. Baker’s team has dominated the competition since 1998 using a computer program which tried different possible shapes and selected the best. His secret was that he added to his computing power by designing a program called Rosetta@home, which could run as a screen saver on the computers of volunteers when they weren’t being used, doing scientific tests all the while. And starting last summer, Baker has added brainpower to computer power, challenging gamers to bend proteins into the best possible shapes in a puzzle game called Foldit.
Biochemists, computer scientists, and game designers came together to create the game, in which users can move parts of the protein according to scientific rules and compete to find the best shapes for each sequence. Players can view their rank and chat online while they play (check out the video below to see how it’s done). As a recent article in Wired magazine argues, this competition can be intense, and the experiment of letting gamers take the reins is working: at the 2008 CASP competition, the gamers held their own against world-class biochemists. Looking ahead, Baker is adapting Foldit to allow players to design new proteins, which could bring serious medical advances. A high score may be something to be proud of for a whole new set of reasons!
I’ll be the first to admit that a lot of the science behind this is beyond me, but then again, that’s one of the great things about citizen science. Not everyone has to be an expert in everything to contribute to valuable advancements in scientific knowledge. The creativity behind this idea and the gamers who make it run is an amazing and vital part of science. Sound cool to you? Then get in on the citizen-sciene action, and download Rosetta@home or Foldit!
-Tim
May 20, 2009 at 12:01 pm
[...] Your Papa? Last week I wrote about Foldit, the computer game that makes gamers into citizen-scientists by letting them [...]