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.
Automating calculations: pKa predictions - I want to compute the standard free energy difference for proton exchange between heliotridane and a molecule which I'll call compound 1 (comp1) heliotrida...
1 day ago