February 1, 2005

The Protein Grid

Continued from page 1

By Karen Epper Hoffman

"I had the idea for some time that Rosetta would be the ideal application for the grid," Bonneau says.

The United Devices grid, with more than three million participants, already runs about a petaflop of computing power -- that means that the system can run 1,000 trillion calculations per second, making the grid about as powerful as all the supercomputers in the world combined. 

Indeed, Bonneau has already had an early insight into how much the grid could speed up the Institute's work: He says his team had been working with Rosetta for two years to get half-way through predicting the structure of a yeast genome -- a project they were able to finish up on the grid in two weeks.

Two Grids, No Waiting

Together, the ISB and United Devices brought in IBM -- with whom United Devices had worked on its previous grid-based smallpox project.  IBM was in the process of setting up its own World Community Grid, which it officially launched in November 2004.

The Human Proteome Folding Project became its first effort -- and indeed the first time grid computing has been used for a biology-related project.

Since its launch, Stan Litow, president of IBM's International Foundation, which helps oversee the World Community Grid, says about 70,000 people have downloaded the software and he expects to have at least one million participants by year end.

"It was so clear that the repetitive calculations [of the protein project] needed the grid," Litow says. "And this was not a narrow projectit has ramifications across a variety of research areas."

With two grids at work, Bonneau says that within six months he hopes to have the database populated with upwards of 100,000 protein "domain" structures -- a "low-resolution" shot of what the protein looks like at the architecture or fold level.  Biologists and medical researchers can, in turn, use that data to get a better (if still not exact) idea of what proteins look like and how they interact. 

Bonneau expressed hope that success in the Human Proteome Folding Project will lead to a second phase, where the grid is used to model a few key proteins to a higher level of detail.  Modeling protein structures down to their atomic detail would give researchers more to work with, but would also be even more computationally intense. 

But for now, the Human Protein Folding Project is a necessary next step to better understanding why our bodies do what they do.

"I really like the idea that this project will have usable, practical results," Bonneau says. "A lot of distributed computing projects don't produce results that people can relate to."