fold it

Fold it is a pretty cool program I found at Lightnir's Blog is. If you are reading this blog it is probably because you are nerdy enough to look at 3D protein structures. If you are even nerdy enough that your idea of a computer game is playing with protein structures, you should check it out. If you do, look for FeLiXe tearing up the high score lists...

This what it looks like. Notice the amazing score of 9577 for this Calcium Ion binding protein. (I am leaving a little head start to lightnir ...)


The producers of the game mention that the computer game strategy may even be a fruitful way of tackling protein folding, which is basically the attempt to find the global free energy minimum structure of a protein. For every geometry you can compute the energy and forces. You can let the forces pull the geometry toward a local energy minimum. But the energy will usually be a very complex function of the geometry with many local minima. And this local minimum may be far away from the global minimum.

One strategy to go on is dynamics. Simulate protein motion at some finite temperature and hope that it will eventually overcome the barrier, leave the minimum, and go to a lower energy minimum.

The second strategy is Monte Carlo. Trying to systematically improve the structure by applying random changes.

The third strategy is making a game out of it and telling people it's fun.

Another interesting trivia about protein folding: Folding a random co-polymer is an NP-complete problem, meaning it has exponential scaling which makes it impossible to use for all but the smallest systems. The reason why in silico protein folding still works in some cases is first that we know the building blocks well and have a big knowledge base. The second reason is that proteins are folding in nature so we should be able to emulate this process and that there is a selection pressure for proteins to fold easily, so it works in nature.

The last thing to wonder about is the question between computer and human problem solving abilities. It will take something like 50 years until we can build something with the processing power of even an ant. Still we are using computers rather than ants for our everyday problems. Well it's because computers are more flexible. But it seems with anything that is remotely related to anything that evolution would select us to do we kick their asses.

Summer

Alright let's go for a non science post. I just spent 8 weeks in the US. The bigger part at UIUC to do some research there. The idea of living on a campus is pretty cool. Just riding your bike to work. Stop by the gym during the day, tons of restaurants. We do not have that back at home. At home I always have to go through the big city with tons of traffic, tons of people,... But of course a big city is also cool.

On my last day I got to see all the ambitious incoming freshmen who still think that life makes sense and that school will take them somewhere. Maybe some even think that research is fun. Maybe because of the fact that it's fun to see how a little, easy sounding task takes up months until you finally have no idea about what you actually did. And when you finally kind of figure out what you are trying to say, putting that in writing takes even longer. Maybe I'll think about it differently when I finally have something published. Because then I can visualize those 10 or 20 people who will eventually superficially sift through the text ...
Well complaining about grad school is a nice tradition that should be upheld.