Fold Your Own Protein

Aaron Mertens
by Aaron Mertens

How many of you have wanted to fold your own protein?

Your opportunity is here!

Let me introduce you to Fold.it, a popular protein folding computer game that has recently been in the news. A few years ago, the University of Washington developed the game that allows players to manipulate proteins or small peptides with the sole purpose of finding the best configuration. The data from the player’s positioning is sent to the University of Washington researchers and is compiled with the goal of discovering the crystal structure of proteins. This process is what recently led researchers to finally develop a model for a sought after HIV-like enzyme. Read more about the story here.

Pretty sweet, eh? It gets better.

Fold

Stanford has a similar protein folding simulation program called Folding@home. Unfortunately, this isn’t a game, but rather it uses the excess processing power on your computer to run thousands of protein folding calculations, and the data again is sent back to Stanford’s research team. A few years ago, I folded my first protein on Sony’s Playstation 3 that had the Folding@home software preloaded. Fourteen hours later, my protein was complete! I felt so accomplished.

Folding@home

Fold.it is able to incorporate human reasoning to the process where the automated Folding@home would need to calculate thousands of shifts and vibrations. For instance, it’s faster for a human to recognize and close the gaps between two alpha helices than the time it takes a computer to run through a thousand different positions before it makes a decision. This is why it took a group of UW students a week and a half to find the full crystalline structure of the viral enzyme, which stumped researchers for 10 years.

For the first time ever, these platforms encourage the public and techies to participate in science and contribute to data intensive research. I invite you to try out the free (and easy) Fold.it on your personal computer or check out some of the awesome things Folding@home is busy developing. Next time you walk by an empty computer cluster on campus, think of all the awesome proteins that could be folded if those computers were utilized.


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