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Planetary News: Search for Life (2007)

SETI@home Spinoff Project Recruits Game Consoles to Decipher Biological Mystery

Click to enlarge > SONY PlayStation 3 The game console is being used to enhance the processing power of the distributed computing project folding@home. Credit: SONY

If you are the proud owner of a Sony PlayStation 3, or are considering purchasing one, keep in mind that your acquisition is much more than an expensive game console. In addition to playing “Dragon Ball Z” with the latest and best graphics, your PlayStation can also aid in the fight against some of the most debilitating diseases known to humankind.

This is because all PlayStation 3 modules, version 1.6 or higher, have been designed to run folding@home, a scientific distributed computing project based at Stanford University. Launched in 2000, folding@home is modeled on the remarkably successful SETI@home, a project launched the previous year thanks to seed funding by The Planetary Society. Like SETI@home, folding@home makes use of a web of thousands of volunteers around the world who donate processing time on their home computers to the project. But whereas SETI@home and all other distributed computing projects have so far contented themselves with the use of volunteers’ personal computers, folding@home is taking things a step further. Data processing will now take place on PlayStation 3 consoles as well, whose processors are far faster and more powerful than those of personal computers.

Folding@home is making use of this powerful computer grid to model one of biology’s most puzzling processes: the folding of proteins. Proteins, composed of long chains of amino acids, are the building blocks of life. In our bodies they both serve as constituent elements of our bones, muscles, and hair, and, in the form of enzymes, are essential for all biochemical reactions. In order to fulfill those functions, however, proteins cannot remain as simple strings, or "necklaces" of amino acids. They need to fold into very specific and complex shapes, or they cannot do their job. One of the most amazing facets of the chemistry of life, and also one of the least understood, is that proteins do exactly that - reliably, efficiently, and quickly. Modeling this process on the atomic scale has proved to be one of the most difficult challenges of computational biology.

The chief difficulty in simulating the folding of a protein molecule is time, explains Vijay S. Pande of Stanford University, leader of the folding@home project. "Small proteins have been shown to fold on a timescale of microseconds [millionths of a second], but it takes an average computer one day just to do a folding simulation of a single nanosecond [one billionth of a second] " he said. At that rate it would take almost three years to simulate a single microsecond of folding, and perhaps a decade or two of computer time to analyze the folding of a single protein. This, computational biologists realized, is hardly practical way of resolving the problem.

It was in this context that the remarkable success of SETI@home caught the attention of Pande and his colleagues. In the eight years since its launching, SETI@home has logged not a decade or two, but millions(!) of years of computer time, searching for a signal from an alien civilization. This kind of computing power would go far towards solving the difficulties in simulating protein folding.

Click to enlarge > Screen of PlayStation 3 running folding@home The screen of the game console shows the actual folding of the protein in real time, as it is deciphered by the processor. The image is three dimensional and can be viewed from any angle. The points of light on the map in the background show where PlayStation 3 units are currently running folding@home. Credit: Stanford University/folding@home

To take advantage of this remarkable potential, Pande and his colleagues launched folding@home in October, 2000. Today, six and a half years after its launch, the project has over 230,000 active users. Of these, over 27,000 are PlayStation 3 users who have added the processing power of their machines to the quest only in the past week, since folding@home started making use of the powerful game consoles. Although they comprise less than one eighth of the machines actively participating in the project, the powerful processors the PlayStation 3 consoleses now provide over 55% of folding@home’s total computing power.

By studying the mysterious process of the folding of proteins, folding@home not only increases our understanding of the biological world but also helps combat devastating and incurable diseases. Parkinson’s disease, Alzheimer’s disease, BSE (“Mad Cows Disease”), and certain types of cancer are all believed to be caused in part by misfolded proteins. Deciphering the exact process by which proteins fold may one day enable scientists to produce synthetic versions of them that could help combat the diseases.

Although Folding@home is still a very long way from producing cures for cancers or Alzheimer’s disease, the project’s contributions to the scientific study of proteins has nevertheless been impressive: Over the past five years, data from folding@home has been the basis for 49 scientific publications.