Spare time? Then fold some proteins

Stanford University scientists have come up with a screen saver that uses thousands of idle computers to assist with simulations of protein folding.

The software, called Folding@Home, is being used by more than 10,000 collaborators and has already led to new information on how proteins fold.

The timescale of protein folding is in the microsecond range, but computers cannot simulate protein folding on that scale.

By using an approach called 'distributed dynamics' to divide the work between multiple microprocessors, the simulation speed is able to be increased to suitable speeds. By using hundreds or even thousands of otherwise idle computers, protein folding can be simulated.

The team, part of Stanford's chemistry department and headed by Vijay Pande, has already used the approach to simulate folding of simple protein structures such as the alpha-helix and zinc finger folds and is using the system to look at several other proteins including the Alzheimer's Beta Amyloid protein and the Engrailed Homeodomain.

The more complicated the protein, the more processors are required to simulate the folding.

Pande's group is also using similar approaches to examine protein design and structure prediction problems as well as RNA folding.

Folding@Home can be found on the group's website, folding.stanford.edu