Thursday, September 29, 2011

Computer games, science and Foldit

Next Monday we will be having our first ever guest post (I know, I know, exciting right?). In anticipation of this great event and because it is loosely related I thought I would mention the following piece of incredible innovation humanity has shown. 

Foldit, is a computer game designed by Seattle based biochemist, David Baker. In the game the player twists and contorts a virtual protein molecule to try to guess its correct, or most efficient, shape. The game itself seems to be quite popular, at least for a small independent game of this nature.

Now ordinarily a game like this might be a quaint example of a clever scientist coming up with an innovative way to make his research more popular and understandable. However, this is not actually the primary aim of Foldit at all. The aim of Foldit is to use the insight and cleverness of the gamers to advance the science itself.

This sounds like a ridiculous idea, but as you can see in the video below, it turns out that the Foldit experiment isn't doing so badly.

And, as explained in this article at Nature News Blog, at an annual competition, intended for biochemists to predict the shapes of proteins, a team of Foldit players did surprisingly well. In fact, they made a genuine scientific discovery. From the article:
Foldit’s biggest success so far came after CASP9 [the annual competition], on an enzyme produced by a retrovirus called Mason-Pfizer monkey virus (M-PMV). A player who goes by the name 'mimi' came up with a shape that would be accurate enough to serve as the basis for determining the real shape of the protein based on X-ray diffraction measurements
"The M-PMV structure had stumped scientists for a very long time before Foldit players made their breakthrough. This is the first example I know of game players solving a long-standing scientific problem," Baker wrote in an email.
You can find the game itself here.

How is this related to the upcoming guest post? Hah, you'll have to come back next Monday if you want to know the answer to that. In the meantime, don't forget to read the comments and join in with the discussion relating to Michelle's post below.


  1. This is a pretty incredible example of how the previously untapped efforts of non-scientists can be used to further understanding! One issue I have with it, however, is that because the number of potential conformations for any given primary protein sequence is so ridiculously high it takes a hell of a lot of time and enthusiasm to actually find the lowest-energy structure. This isn't the sort of game where lots of people each playing for a small amount of time will be useful, you need people to really get a bit obsessed, as with the woman in the video! Whether that's a good or bad thing is a separate issue altogether.

    It's also worth pointing out that this approach most likely wouldn't work for the majority of proteins because they seldom fold entirely independently of other factors. Many are integral membrane proteins and so are stabilised in otherwise energy-high conformations by membrane phospholipids; others only fold correctly with the help of chaperone proteins that get them past an energetic barrier to correct conformation; and most proteins also interact strongly with other associated proteins, which have a significant effect on their folding.

    That said, I like the idea behind the game, and it's clearly effective in some cases if it's provided a molecular replacement strategy for this M-PMV enzyme!

  2. The way I understood the process was that it wasn't the gamers entirely predicting the protein structures, so much as gamers being directed to focus on specific areas of the protein to help a computer algorithm to know where to look. Thus reducing the number of shapes that the computer has to search through and allowing it to find the correct shape quicker.

    Even that though probably takes a reasonable amount of commitment from the gamer before the algorithm gets any benefit from the gaming.

  3. This article here: also shows how other internet based games are using enthusiastic people with a lot of spare time on their hands to solve other problems that can't be achieved with automated programmes. Perhaps if the Foldit game involved saving small lemming-type creatures, then I'd be more interested in playing it ...

  4. PS: What's up with the time stamp on the blog? I'd like to point out that it's actually 12pm, I'm not reading this blog at 4am in the morning.

  5. Shhhh, If google hear you talking about the great state of California's timezone like that we might get excommunicated.

    Thanks for the link too. It's amazing how creative humanity can be at solving problems. Many of the captcha's that the internet makes you fill out nowadays are apparently doing a similar thing:

    I'm racking my brain to work out how to turn my research into a clever game. "Find the missing galaxy cluster", perhaps?. "Which picture is the real universe?", "Destroy the antimatter!"