Foldit

Have you seen Foldit? It’s a video game where the goal is to fold proteins. Protein folding is a very interesting problem. If you sequence DNA, you can get an ordered list of the amino acids which make up a protein, but that doesn’t tell you the 3 dimensional shape of the protein. That’s what you really want to know, but it is very hard to figure out. A chain of amino acids could fold in an enormous number of ways. The trick is to find the one which happens in nature. This is basically a very complex optimization problem.
There are a number of techniques which are used to calculate this optimization problem, but they’re all very slow and inefficient. The developers of Foldit believed that since humans can currently do it better than software, the best approach would be to get lots of humans working on the problem. How do you get lots of humans to work on something? You turn it into a game. That’s what they did. When you run Foldit, it gives you a 3D view of a protein and lets you bend and twist it. Your goal is to bend it into a shape which has a higher score than anyone else. It’s actually a lot of fun.

There’s a new paper coming out in Nature’s Structural & Molecular Biology journal which is based on work done in Foldit. It proposes a structure for a retroviral protease in M-PMV (a virus which causes cancer in monkeys). This protein is a test case from CASP9. This makes it a good one to benchmark the Foldit approach with, because lots of other solution techniques are being applied to it. It currently looks like Foldit did very well compared to other approaches.