Tuesday, September 20, 2011

Brody's Notes... Online Video Gamers Crack AIDS Enzyme Puzzle

FoldIt 3D M-PMV retroviral protease model
By Brody Levesque | SEATTLE, WASHINGTON -- Utilising the specialised computer video game Foldit, developed by researchers from the University of Washington in 2008, on-line video computer gamers figured out how to decipher an enzyme critical to the early development of AIDS that had stumped scientists for nearly ten years.
According to Dr. Firas Khatib of Washington University's biochemistry lab, players created an accurate model of a particularly tricky enzyme in "less than 10 days." Most importantly, the enzyme in question comes from an AIDS-like virus that affects Rhesus monkeys and could possibly open the door for treatments to that horrific disease.
"We wanted to see if human intuition could succeed where automated methods had failed," Khatib said. "The ingenuity of game players is a formidable force that, if properly directed, can be used to solve a wide range of scientific problems."
One of Foldit's creators, Seth Cooper, explained why gamers had succeeded where computers had failed.
"People have spatial reasoning skills, something computers are not yet good at," he said. "Games provide a framework for bringing together the strengths of computers and humans. The results show that gaming, science, and computation can be combined to make advances that were not possible before."
In Foldit, players are presented with a series of brightly colored pieces that represent individual molecules. The rules of chemistry are built into the game, setting the stage for players to strut their stuff folding the molecules into the lowest energy configuration. As the energy gets lower, the score rises, and so go the mechanics of the game. Understanding the folded shape is vitally important for researchers, especially when creating drugs to stop dangerous diseases.
12 to 15 gamers called the Foldit Contender Group (not so far removed from a guild) came together and provided an accurate 3D rendition modeling the crystal structure of the M-PMV retroviral protease, which in plain English, is an AIDS-like virus found in monkeys. Figuring out the structure will allow scientists to develop drugs whose molecular structure targets and locks onto those proteins responsible for spreading a disease.In this case, the enzyme in question belonged to a group of enzymes called proteases that help the virus spread.
Zoran Popovic, director of University of Washington's Center for Game Science, believes this is a new frontier for gaming and science:
"Foldit shows that a game can turn novices into domain experts capable of producing first-class scientific discoveries. We are currently applying the same approach to change the way math and science are taught in school."