Foldit: Curing Diseases, One Video Game at a Time

By: Sam Laughlin

Most people growing up today have faced the problem.  It is the bane of teachers, parents, and employers around the world.  The problem is simple: kids today and their video games.  Teachers say they make you stupid.  Parents argue they make you blind.  Employers think they make you lazy.  They would all agree video games have no use in a productive society.  Fans of video games have little evidence to counter the almost constant barrage of negative, nerdy accusations that their pastime is a waste of time.

Until now.

A humble group of computer scientists and biochemistry researchers based out of the University of Washington has created a video game, a puzzle game that, at first, seems very simple.  Players move three-dimensional representations of protein strands around, waving ends and bits here and there, until the proteins line-up in a particular way, rewarding the players with fanfare, fireworks, and high scores before moving on to the next puzzle.  The music is chipper and the graphics are quaint and cute.

But the cuteness is deceiving.  These puzzles reach beyond the typical video game problems of saving fictional princesses from fictional castles in fictional mushroom lands.  These puzzles are fighting viruses.  Real viruses.

This is Foldit, a free-to-play downloadable game that bridges players bored at work with scientists attempting to cure some of the most lethal diseases that affect mankind.  Over 200,000 people have played it, and that number grows every day. 

Users of Foldit are helping figure out the complexities of protein strands like the one above

Dr. Seth Cooper has worked on the Foldit project for four years, an attempt to solve questions that scientists and computers were failing to answer.  It works by combining real protein-related problems facing real scientists, shaped by Dr. Cooper and his staff of programmers into puzzles, then plugged into the Foldit program.  Players then take part in competitions to solve the protein.  Whoever has the highest score wins the puzzle.  This protein, now reworked by human hands, is delivered back to the scientists, who then use it to aid their research.

Proteins wear many hats: armed guards fighting invaders, transporters, and certain ones that act like mail clerks, sorting through endless messages and passing them along to their destinations.  Protein molecules serve a bedrock role in shaping life.  For molecular biologists, understanding how proteins work is essential to defeating viruses, but understanding proteins means an understanding of their shape.  Proteins love to bend, twist, and tweak themselves in almost incalculable ways.  In fact, they are so twisty, bendy, and weird that reshaping their structures has proven totally confounding for scientists and computers alike.

Scientists have attempted to out-source protein folding before, using programs such as Folding@home for the Playstation 3, and Rosetta@home, a PC-based folding program also created by the University of Washington.  But these programs only add people’s unused computer power to help compute protein problems.  They don’t fix the bigger issue.  Computers can’t think outside the box.

“The computer doesn’t really see these things in the same way that people do,” says Dr. Cooper.    The computer moves shapes logically and mathematically, following complex algorithms.  It solves a protein up to a certain point, then it consider the job done.

“But really,” Dr. Cooper explains, “if it made a sort of more drastic move, it could have found something better.  It’s something we’ve actually seen, where what people are able to do is actually make the structure of the protein worse in the short term, but in the long term, make the protein fold up much better than where they started.  So people have this longer-term ability of intuition and ability to stick to their ideas of what would make the protein fold up better.”

One such protein proving a difficult time for computers and biologists alike was one attached to the AIDS virus as found in Rhesus monkeys.  Scientists had toiled for ten years building a load of experimental data.  They only needed the shape of that one protein.

“We presented the structure to the players and they were actually able to come up with a structure that was accurate enough to solve and confirm the experimental data that the scientists had,” says Dr. Cooper.  This protein was then passed back to the scientists, “so what they can start to do is look at the shape of the protein, how it works, and try to maybe come up with drugs or other proteins that would inhibit the function of this protein that the players solved, and try to design sort of new anti-retro viral drugs.”  While only overcoming a single obstacle towards a cure, the achievement is significant, not to mention the result of a video game, played by regular people.

The “game” side of Foldit has proven as difficult as the “science” side.  “It’s hard enough to just make a fun game in the first place, right?” says Dr. Cooper.  “And then once you add on top of that the fact that this has to actually produce something real, you know, the mechanics of the game have to be scientifically accurate, in a sense, at the molecular level, is actually a very large constraint put on the design of the game for this particular game… so there’s definitely a conflict between those two goals.”

That difficulty has led to Foldit’s endless development, with sporadic refinements, tweaks, and retouches.  “The game is constantly changing and evolving and improving,” says Dr. Cooper.  “It’s not just a static game.  If you played the game last year, and you play it now, you might find there is a lot of new and different things within the game.”  Foldit is now experimenting with allowing players to create new proteins, ones not found in nature with exciting new uses to medical science.

Bringing science and gaming together holds a world of potential for Dr. Cooper and his team, who are presently expanding to new projects that include nanotechnology.  This new game, “similar to Foldit, will actually give players the ability to design little machines at the nanomolecular scale,” Dr. Cooper said.  Tiny molecular motors, machines, and computers, designed by gamers and built by scientists—“Yeah, there’s a lot of potential for this kind of approach.”

So next time you find yourself feeling the burning desire to procrastinate, kick your shoes off and try playing a video game.  Who knows, you might cure cancer.

Foldit can be downloaded, for free, from http://fold.it/portal/ for Mac or PC.  Like, right now.  Go Foldit.

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