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Gamers help protein 3D structure modeling

One of the goals of computational biology is to predict the complete high-order structure of a protein from its amino acid sequence. Often reasonably good structures can be produced by modeling a new protein according to an already-known structure of a homologous protein, one with a similar sequence and presumably a similar structure. However, these structures can be inaccurate, and obviously this method will not work if no homologous structure is known.

 

Foldit is an online game developed by the research team of Dr. David Baker that attempts to address this problem by combining an automated structure prediction program called ROSETTA with input from human players who manually remodel structures to improve them. Even though most of the players have little or no advanced biochemical knowledge, Foldit has already had some striking results improving on computational models. A paper in Nature Structural & Molecular Biology details some interesting new successes from the Foldit players.

 

Does this prove that gamers know more about folding proteins than computers do? Some of them might, but Foldit doesn’t really use human expertise. Rather, the game uses human intelligence to identify when the ROSETTA program has gone down the wrong path and figure out how to push it over the hump. When the human intelligences aren’t daring enough, or trust the system too much, Foldit doesn’t do any better than completely automated structural methods. When the human players are encouraged to challenge the computational results, however, the results can be striking. As Baker’s group are clearly aware, further development of the program needs to be oriented towards encouraging players to go further afield from the initial ROSETTA predictions.

 

The complete article by Michael W. Clarkson is at:

http://conflux.mwclarkson.com/2011/09/foldit-pmv-pr/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+ConformationalFlux+%28Conformational+Flux%29

 

The paper describing Foldit players results is available directly from David Baker's lab:

http://www.cs.washington.edu/homes/zoran/NSMBfoldit-2011.pdf

 

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