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Gamers fold retroviral protein

November 26, 2011

In a scene out of Frontera College, the free on-line computer game  Foldit allows you–anyone–to help discover protein structures.  By playing the game, you improve the model of crystallography-based structures for key medical proteins such as those of viruses. Improved structures help medical researchers design better drugs. Recently Foldit players obtained the structure of a retroviral protease for a simian AIDS-causing virus, MPMV. The solution took three weeks generating more than 60,000 models (above).

Have you tried playing Foldit? Are there other crowdsourcing opportunities out there to assist medical research?

  1. alex tolley permalink
    November 26, 2011 7:08 pm

    The FoldIt approach is a departure from the more usual distributed computing approach first started by SETI. I am not aware of another medical application, just the Galaxy Zoo which has people identify galaxy types.

    Crowd sourcing vs brute force computation depends on how hard the problem is to solve. Can it be solved algorithmically or not. Humans are very good at pattern detection, so the Galaxy Zoo task makes sense. I certainly would not have thought humans could exceed machines for protein folding and therefore would have opted for the distributed computing approach.

    • November 26, 2011 11:43 pm

      Pattern detection is the key thing for proteins. Different proteins have recurring “motifs” with common functions, such as receptor binding, reaction catalysis, and DNA fitting. In molecular biology class at Kenyon, undergraduates learn protein patterns by illustrating their own molecule:

      Other kinds of distributed computing are used in life science, but it’s fascinating that humans still have the edge for finding protein patterns.

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