Monday, August 23, 2010

Solving protein folding - humans outperform computers

I remember from my graduate student days in the 1960's attending biochemistry lectures in which the professors expressed confidence that we would soon know the algorithms for predicting from the linear sequence of amino acids in a protein the three dimensional shape into which it would fold. That goal has seemed to recede from view despite increasing effort with sophisticated supercomputers. (The problem is that even a moderately sized protein can theoretically fold into more possible shapes than there are particles in the universe.) It turns out that Foldit, a multiplayer online game that engages non-scientists, is now yielding more accurate predictions of correct protein folding than one of the best known computer folding programs, Rosetta@home, which was created by molecular biologist David Baker at Univ. Washington, Seattle. (The program distributes its calculations to thousands of home computers around the world, automatically sending the results back to Baker's lab.) From the abstract of the Cooper et al. paper on their Foldit game: Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues. Players working collaboratively develop a rich assortment of new strategies and algorithms; unlike computational approaches, they explore not only the conformational space but also the space of possible search strategies. The integration of human visual problem-solving and strategy development capabilities with traditional computational algorithms through interactive multiplayer games is a powerful new approach to solving computationally-limited scientific problems.
Two useful reviews summarize this work, one in the NYTimes, the other in Science Now.

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