Randall A. Gordon

There have been many distributed computing projects around for years. Basically these projects work by sending out data to many computers to do calculations on in the computer’s spare time. It started with Distributed.net attempting to crack MD5 encryption with brute computing force. As Distributed gained popularity other projects started popping up en masse. The SETI@home project focuses on detecting interstellar communications from across the universe by sorting through massive amounts of radio telescope data. One project I personally participated in was the Great Internet Mersenne Prime Search, also known as GIMPS, searched for a specific type of prime number called a Mersenne prime (if you hadn’t already figured it out from the name of the project). There are several projects which attempt to solve the puzzles of protein folding. One of them is Rosetta@home.

But what do you get when you take the Rosetta engine and apply game theory to it? That would be a new type of distributed computing project called Fold It. As their tag line says, “Solve Puzzles for Science”, the game is a series of protein folding puzzles. The first puzzle can be seen at the right. The gist of the game involves reorganizing the amino acids and backbones of the proteins. You move them into configurations which are compact while requiring as little energy as possible to maintain such a configuration.

As the game progresses the puzzles become more difficult as the proteins which are presented become more complex. If there are people out there who simply can “see” how proteins work in their mind’s eye–protein savants–then this game could catapult protein research forward.

The Fold It site mentions that there will be a feature added over the summer that will allow for players to “design” proteins. Models which work in the Rosetta simulator can then be synthesized in the lab. This aspect of the project is most intriguing to me. It opens the door for anyone to have the chance at creating a protein which could be the key to curing AIDS, solving the world’s energy crisis or any number of issues.

If you would like the chance at helping with cracking one of the most important scientific problems biologists are currently tackling, have a look at Fold It. So far, I’m having a blast folding!