There was a time when computers were used solely for scientific purposes. Of course the everyday man didn’t call it a ‘computer’ back then, but a ‘room’.
Later on, computers were thrown onto the general market. It wasn’t long until the very first games appeared. Pong led the consumer into a new era, and he didn’t stay alone that long.
After a while other games popped up; games you had to enter into the computer yourself, like hangman. They were soon followed by those ‘revolutionary’ floppy disks. Time sped up, and we were playing HiRes Crysis on our CRT monitors sooner than we originally anticipated.
All those overpowered machines in the hands of everyday consumers – and we use them for… playing games? Isn’t that a bit overkill? The overall attitude would be to shrug and go back to those games, but a new trend is rising and it’s popping up in more and more places.
The best known example is probably Folding@Home for the PlayStation 3. This one uses your console’s processor power (during inactive times) to create one big super computer. This supercomputer then starts working on scientific projects, like molecular folding.
Another possibility, and the one we’ll be looking at today, is foldit.
Solve puzzles for science. These fun puzzles aren’t of the kind you’ve probably played with during your childhood, but are in fact proteins.
Proteins are little organic factories that can be found in cells of every living thing. You can see them as the factories that keep a land standing. Without proteins you wouldn’t be able to survive.
These proteins are made of amino acids. They are the building blocks of the factories, the bricks. Each of these amino acids has a small group of atoms, hanging besides them like limbs. To form a protein, all these amino acids are holding hands.
So how do I solve a protein?
Now imagine that these amino acids are all small children, say four or five years old. Instead of standing in a proper line, they’re all over the place.
Your task is to hand out some discipline. Create a more compact group, make sure little Tom’s elbows aren’t where they’re not supposed to be, and so on.
There are several tools you can use to fold the protein. These include:
Shake: this one makes sure none of the sidechains clash (e.g. Tom’s elbow)
- Rubber band: this literally puts rubber bands between pieces of the protein
- Wiggle: this one tries to put the protein in a better, more compact state. It also pulls the rubber bands tighter, if applied. Note that a computer ‘wiggle’ can never solve the puzzle as good as a human.
The player gets awarded points, the major part of them for compactness. A minimum is stated for each level, but you shouldn’t stop there if you want to advance in the rankings.
And how does this help science?
A protein string always returns to a specific form; the most stable one. By solving these puzzles, a database with all the different folding possibilities is created. Using all these user ‘solutions’, one can try to approach the ‘ideal’ protein form.