Fold.it

So... I've been a long time proponent of Folding@Home. Its a good project that takes your extra CPU cycles and donates them to research protein folding. According to the site some of today's diseases, like Alzhiemers, Mad Cow, and Huntingtons are the result of proteins folding incorrectly. The project uses distributed computing to help crunch large amounts of data in a reasonable time because individuals, like me, donate extra CPU cycles.

The reasons for it are actually posted on this site:

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Why is protein folding so difficult to understand?

It's amazing that not only do proteins self-assemble -- fold -- but they
do so amazingly quickly: some as fast as a millionth of a second. While
this time is very fast on a person's timescale, it's remarkably long for
computers to simulate. In fact, it takes about a day to simulate a
nanosecond (1/1,000,000,000 of a second). Unfortunately, proteins fold
on the tens of microsecond timescale (10,000 nanoseconds). Thus, it
would take 10,000 CPU days to simulate folding -- i.e. it would take 30
CPU years! That's a long time to wait for one result!

I couldn't agree with the quote more, that is a long time to computer a single result. This makes me believe that this problem is one known as an NP problem. Its an easy explanation as to why it would take so long to get just a small period of real time computed. So, like all these kinds of problems, the question is asked “How can we speed things up?” Currently the way to try and solve this particular problem has been to throw more technology at it. There are now versions of the program that user a computer's GPU to do these computations faster. Which has been known to show a significant improvement from the number crunching standpoint, however there is now another way.

This is where fold.it steps into the picture. Instead of using extra CPU cycles, fold.it turns the problem protein folding research into a game. Yes you heard me correctly, a game. As I understand things, players choose a puzzle, which is a protein that has already been folded, and the player that folds a particular protein closest to the natural protein wins points that particular puzzle, the top five or so players get points in the ranking system.

So I encourage you all to open an account, and play a couple of rounds of this interesting game for science. Or to show that you can fold a protein better than a computer. Oh, and don't forget to add me to your buddy list.

Happy folding!

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