Sunday, May 18, 2008

Protein Folding with FoldIt

I have a new obsession :) Those who know me well have seen me do this many, many times. A new shiny thing comes along and I'm absolutely bonkers about it for a few weeks before moving on to the next thing. My new favourite is called FoldIt and it's a protein folding simulation.

Wow. Protein folding....mmmm...cancel the trip to Disney kids, lets fold protein instead! Whatthehell?

It's a game built around a real scientific problem, that of predicting what physical shape a teeny-tiny protein will fold into in nature. This is important because their shape determines their function, and by knowing the exact shape of a protein, you'll be able to tell what it will do inside a living being. It might cure you or kill you, or do nothing. Or cure cancer. The fly in the ointment is that it is astoundingly difficult to know what shape a protein will take. As you play the game, it calculates your score based on how much energy it takes for the protein to hold that shape (lower is better), and your score is immediately shared online against every else's best score, so there's a real feel of friendly competition.

By learning to play the game, you're also taking part in an experiment to see if human intuition about the way shapes fold together is better than the current automated 'brute-force' approach used by computers, which basically try every position they can think of and see which one is best. This takes a very long time and gets ridiculously slow on large proteins.

You can see videos of the game in action here and when I got a chance to ask one of the developers if the game had worked; if we'd come up with good protein designs quickly enough, he said they'd been blown away by how well we'd done. He didn't have time to elaborate, but I'd say that's good news. We'll soon be put into the CASP challenge, a biannual competition to see who's software can compute protein shapes the most accurately. It'll be very interesting to see if a swarm of barely trained people playing with shapes can beat the automatons, won't it?

It's really got into my brain and I've played it a lot this week: there were two nights I skipped dinner! I've got the current high score on a few of the current puzzles and top ten scores on several others, so I guess I've figured out some tricks that work pretty well. Eventually the developers want to figure out how to capture those "tricks" and put them into their software (which you can run on PC at home without even knowing its there - do it!)

No comments: