Montag, 19. September 2011

Online game players help solving protein structure

For some time, there have been projects like SETI@Home, where
people donate their computer resources to help crunching numbers
for scientific projects.

Now, donating their own brain power, online game players
have helped to find the correct structure of a protein.

The idea in protein folding is that the protein molecule will fold
into the shape which minimizes the overall energy. Unfortunately,
there are a lot of "local minima" in which any computer algorithm
might get stuck - a configuration which is not easily improved by
small steps but still far from ideal.

Now gamers at a site called Fold.It have
tinkered around with some protein structures and found a particular
structure for some special HIV-relevant protein that scientists had
not been able to correctly decipher before. The resulting Nature
paper is here:

Nature Paper on FoldIt Structure

One has to say that still a lot of expert know how went into this:
both into presenting the players with some reasonable starting points,
and with taking the final structure the players came up with and
doing the last few improvements on a computer (and, of course, experts
wrote the game). Still, it is impressive. The Nature paper even
shows a graph of protein structure quality versus time, with some
jumps highlighted where particular players had smart ideas to improve
the structure.

This one obviously benefited from people's insight into spatial
problems and from heuristic reasoning that can overcome the
problem with getting stuck in local minima. One wonders which other
scientific problems are amenable to this kind of treatment
(which is unlike the dumb brute force approach where one makes
computer users pick out galaxies from astronomical pictures, say).

It would be even cooler (but also more expensive) if players' actions
did not just perform operations on a computer but really did something
in the lab (mixing selected chemicals in different places of a
microfluidic chip and see what happens...).

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