Protein-Folding Computer Game Could Benefit World Health

A new computer game turns protein folding, a key investigational process for solving biological mysteries ranging from Alzheimer's disease to vaccines, into a competitive sport that may even help find a cure for HIV.

The new game, named Foldit, was developed by researchers at the University of Washington (UW, Seattle, USA). The game, at an introductory level, teaches the rules; after about 20 minutes of training, participants feel as if they are playing a video game, but actually are clicking their mouse in the service of science.

Proteins form every cell, make up the immune system, and set the speed of chemical reactions in the human body; however, of the over 100,000 different proteins that exist, there are only a few in which their complex geometrical shapes are known. In many more, the surface anatomy that plays a crucial role in their biologic function remains a mystery. Computer simulators can calculate all possible protein shapes, but this is a computationally complex mathematical problem so intractable that it would take computers centuries to solve.

In 2005, a project named Rosetta@home that taps into volunteers' computer time around the world was developed to help solve the structure of smaller proteins, but as the protein gets larger it becomes much more difficult to solve, and computers often fail at it. Both Rosetta@home and Foldit use the Rosetta protein-folding software. However, Foldit is the first protein-folding project that asks volunteers for something other than unused processor cycles on their computers or Playstation machines. Foldit also differs from recent human-computer interactive games that use humans' ability to recognize images or interpret text; instead, Foldit capitalizes on people's natural three-dimensional (3D) problem-solving skills. Eventually, the researchers hope to discover protein-folding prodigies who have innate abilities to see proteins in 3D.

The game itself looks like an advanced version of Tetris, with multicolored geometric snakes filling the screen. A team that includes six UW graduate and undergraduate students spent more than a year discovering how to make the game both accurate and engaging. Almost 1000 players have tested the system, playing informal challenges using proteins with known shapes. The developers have opened the game to the public, offering proteins of unknown shapes for solution; Foldit gamers will eventually face-off against research groups around the world in a major protein-structure competition to be held every two years. Eventually, the researchers hope to present a medical nemesis, such as HIV or malaria, and challenge players to devise a protein with just the right shape to lock into the virus and deactivate it. Winning protein designs will be synthesized and tested in petri dishes. High-scoring players will be credited in scientific publications the way that top Rosetta@home contributors already are credited for their computer time.

"Long-term, I'm hoping that we can get a significant fraction of the world's population engaged in solving critical problems in world health, and doing it collaboratively and successfully through the game,” said team member Professor David Baker, Ph.D., a UW professor of biochemistry and developer of the Rosetta@home project. "We're trying to use the brain power of people all around the world to advance biomedical research.”


Related Links:
Foldit
Rosetta@home
University of Washington