Foldit - In the name of science, solve thy puzzles!


Updated: November 12, 2014

Protein folding is one of the big challenges in modern science. In a nutshell, the fine arrangement of molecules into protein shapes determines their functionality. It may work, work badly, or not at all, and it comes down to angstrom-alignment between different bits and pieces, caused by the forces of physics. If you know the exact folding pattern, then you can essentially control the protein as you see fit.

Sounds easier than it is. Indeed, millions of computers worldwide are busy trying to fold proteins 24/7, testing a virtually endless number of folding options. It's done scientifically, without direct human input. However, a bunch of scientists is testing a possibility of using humans as a far more efficient alternative. In other words, we could use our spatial awareness to figure out geometric alignments in seconds, which could take a typical computer years to solve. Which is where Foldit comes in.

Teaser

Foldit, foldit good

Foldit is a gaming science application designed to help the scientific community find the best way of folding proteins. The hypothesis is that humans can solve protein folding puzzles with the understanding of the complex 3D space and object placement, something we've spent the last few million years learning and perfecting. And that humans can do this with greater efficiency than algorithmic machines. Sounds great.

I setup Foldit on an Ubuntu box. The program won't run without freeglut3 package installed, and even then, I did not have any audio. But that's a relatively minor niggle.

When you launch the program, you will be asked to register, and then go through a first sort-of tutorial puzzle. You're given an abstract protein shape. You do not know what it is, but those little arms are probably amino acids. Anyhow, you need to pull protein ends this way or that to resolve chemical-bond conflicts that prevent it from being a functional protein or those that cause it to act in a malicious way.

Start

Tutorial, sort of

Puzzle completed

As you make progress, you gain additional features and perks. It's meant to be a game, so it's meant to be fun. Puzzle solving is a natural human tendency, so the idea is to do real science without the pain of real science. Overall, it works well. The GUI could be a little more polished and smoother, but there were no outstanding issues. Apart from the actual challenge of making it all work in the 3D space. And efficiently. For example, in the third level, I did fix all the clashes, but not well enough, and I needed the shake tool helper to get past the problem. I mean I could have played some more, but it illustrates the point.

Getting difficult

Getting complex

Conclusion

Foldit seems like an interesting and rather fun tool. It's not as exciting as some first person shooters or fully fledged strategy games, but if you do like tricky 3D puzzles and you do not mind helping the science, this could be a game for you. Just imagine what your mind can do, and how it interprets the space, and how dumb the computers really are. That should give you the pleasure and the sense of superiority when playing. Oh, yes, the game offers competitions and time-limited challenges, so there's that, too.

Overall, I laud the effort behind Foldit. It's a very interesting concept. We may yet discover that although computers are immensely advanced and powerful, they still lag behind in some of the areas that we perceive as utterly natural and simple, like shape recognition and spatial arrangement. Well, this is your chance to do some good for the world. Maybe solve some cancer with your next puzzle, who knows.

Thanks to Ivana for the recommendation!

Cheers.

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