New Computer Game Promises to Help Make Medical Breakthroughs

Now all those years of playing Tetris in one's free time may not be totally wasted. University of Washington researchers have released a game named Foldit that aims to harness the puzzle-solving skills of computer users worldwide in making medical discoveries.

Doctoral student Seth Cooper, postdoctoral researcher Adrien Treuille, and associate professor Zoran Popovic--alNl of the University of Washington's computer science and engineering department, teamed with David Baker, a UW biochemistry professor and Howard Hughes Medical Institute Investigator, worked together to develop the game. The researchers spent more than a year designing the game and incorporating the advice of professional game developers.

Foldit employs users' three dimensional problem-solving skills in folding proteins, a task that has occupied structural biologists for years. Proteins, essential components of life, are biological macromolecules made up of linked building blocks known as amino acids. The long amino acid chain that makes up a protein folds into a specific shape that determines the protein's structure and function within an organism. The human body contains over 100,000 different types of proteins, all of which perform different duties, ranging from controlling biological processes to making up the structure of cells.

Though researchers already know the amino acid sequences of many proteins, they have more difficulty determining how the protein strands are folded into the three dimensional shapes that enable them to carry out their functions in the body. The creators of Foldit hope that their game may help scientists work on the problem of protein folding.

Foldit, available free for download at http://fold.it, teaches players the basics of protein folding and tracks progress through a scoring system related to the stability of the protein structure: the more stable the folded protein structure according to the laws of physics, the higher the player's score. Players increase their score by clicking and dragging on parts of the protein, depicted as a branched, kinked strand, to change the shape of the protein and increase its stability. After completing the game's tutorial levels, players are then presented with puzzles: more complicated proteins to fold into the most stable structure possible.

Foldit expands on earlier attempts to take advantage of the pooled resources of online personal computer users in structural biology research. In 2005, Baker released Rosetta@home, a computer program that, when downloaded and run on a personal computer, takes advantage of the computer's unused computing resources to simulate possible folded protein structures. The combined processing power of many users' personal computers, pooled through the Internet, are then available to tackle protein folding problems. Ultimately, however, because of the large number of possible protein structures, the simulation needed more than the combined resources of 200,000 volunteers' computers to effectively solve all protein folding problems, according to Baker. "An approach like Rosetta@home," he said, "does well on small proteins, but as the protein gets bigger and bigger it gets harder and harder, and the computers often fail."

The success of Foldit, in contrast to Rosetta@home, relies on humans to help where computers fall short in calculating protein structures. Chess and other strategy games have previously demonstrated that humans are more adept than computers in coming up with creative solutions for problems. With Foldit, researchers hope to make the search for ideal protein structures more efficient by harnessing this human creativity.

"People, using their intuition, might be able to home in on the right answer much more quickly," Baker said.

Popovic hopes Foldit will play a part in future medical discoveries. "Our ultimate goal," he said, "is to have ordinary people play the game and eventually be candidates for winning the Nobel Prize."

Written by Amy Liu

Reviewed by Jeffrey Kost

Published by Pooja Ghatalia.

JYI has a science journalism program, which trains undergraduates how to write news and feature articles about science and about how to communicate effectively to the public.
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