tags: biochemistry, protein folding, computer science, Foldit: Biology for Gamers, Fold It, citizen science, computer games, David Baker, Zoran Popovic, nature, University of Washington, streaming video, bpr3.org/?p=52,peer-reviewed research, journal club
Guessing how a protein will fold up based on its DNA sequence is often too complex for even the most powerful computer programs. Now biochemists and computer scientists at my alma mater, the University of Washington, have collaborated to create Foldit, a free online computer game where online gamers do the work.
David Baker, a professor of biochemistry at the University of Washington and co-author on this paper, and his colleagues previously designed a computer program called Rosetta@home. That program relied on the power of idle computers to evaluate many thousands of different structural possibilities as it seeks out the optimal energy state for various protein structures. But computers cannot make intuitive leaps in logic or spatial reasoning, so Rosetta@home volunteers quickly became frustrated by the painfully slow progress of the structures they observed on their screen savers.
“People started writing in saying, ‘I can see where it would fit better this way’,” remarked Dr Baker.
Dr Baker and his collaborators responded to their volunteers' advice and thus the computer game, Foldit, was born. Foldit is an open access computer game that allows users to manipulate different parts of a protein to optimize the stability of its 3-D structure. It has been compared to another popular online game, Tetris, but instead of stacking blocks, players fold a protein.
The game comes with a tutorial narrated by a cartoon version of Dr Baker that teaches the basics of protein chemistry such as how to align your beta-pleated sheets to allow hydrogen bonding to form, and how to prevent your side chains from crashing into each other.
Like all engaging computer games, Foldit has addictive appeal: players earn points based on the internal energy of their protein's 3-D structure, and every protein puzzle has a high score that players can try to best. As their scores increase, players move on to more challenging levels of play, and they can compete -- or intriguingly, they can collaborate. Collaboration between top players can result in innovative protein folding strategies.
“There’s this incredible amount of human computing power out there that we’re starting to capitalize on,” states Dr Baker, who changes his Rosetta algorithms to adopt some of the best of these human innovations. Rosetta, developed Dr Baker, carries out the Foldit energy calculations.
The Foldit players (known within the group as "folders") have not -- yet -- designed any proteins might cure Alzheimer's Disease or HIV/AIDS, but this citizen science project utilizes so much human brain and computing power involved that it is only a matter of time before these and other medical issues are addressed. To honor their Foldit players' dedication and ingenuity, the authors' acknowledgment list at the end of the paper includes the names of the more than 57,000 Foldit players -- longer than the paper itself! [Watch the video to "meet" some of the scientists and the folders]
"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," reports Zoran Popovic, associate professor of computer science at the University of Washington and co-author on the paper.
Perversely, despite the fact that this is a digital citizen science project, the paper written about it is not Open Access. But you can purchase a copy!
Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010). Predicting protein structures with a multiplayer online game. Nature, 466 (7307), 756-760 DOI: 10.1038/nature09304.
FoldIt Blog: Solve Puzzles for Science!