Simulating protein folding is often considered a "holy grail" of computational biology, he added. "This is an area of hot competition that includes a number of heavy weights, such as IBM's $100-million, million-processor Blue Gene supercomputer project."

Folding@home

Two years ago, Pande launched Folding@home a distributed computing project that so far has enlisted the aid of more than 200,000 PC owners, whose screensavers are dedicated to simulating the protein-folding process.

The Stanford project operates on principles similar to earlier projects, such as SETI@home, which allows anyone with an Internet connection to search for intelligent life in the universe by downloading special data-analysis software. When a SETI@home screensaver is activated, the PC begins processing packets of radio telescope data. Completed packets are sent back to a central computer, and new ones are assigned automatically.

For the Nature study, Pande and Snow a biophysics graduate student asked volunteer PCs to resolve the folding dynamics of two mutant forms of a tiny protein called BBA5. Each computer was assigned a specific simulation pattern based on its speed.

With 30,000 computers at their disposal, Pande and Snow were able to perform 32,500 folding simulations and accumulate 700 microseconds of folding data. These simulations tested the folding rate of the protein on a 5-, 10- and 20-nanosecond timescale under different temperatures. Using these data, the scientists were able to predict the folding rate and trajectory of the "average" molecule.

Experimental verification

To confirm their predictions, the Stanford team asked Gruebele and Nguyen to conduct "laser temperature-jump experiments" at their Illinois lab. In this technique, an unfolded protein is pulsed with a laser, which heats the molecule just en
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Contact: Mark Shwartz
mshwartz@stanford.edu
650-723-9296
Stanford University
21-Oct-2002