Rosetta@home puts the "boink" back in biochemistry

In the field of molecular biology, the search for the proverbial needle in the haystack has been delegated to computers --- your computers.

The Rosetta@home project, led by UW biochemistry professor David Baker, utilizes BOINC software developed at the University of California, Berkeley to predict the structures of naturally occurring proteins from their amino acid sequences. This technology can be used to design new proteins that fight HIV, malaria, cancer, Alzheimer's and more. Several recently released predictions are proving to be encouragingly accurate, Baker said.

BOINC (pronounced "boink") is an open-source program that can be installed on any private computer. The program uses the idle processing power of individual computers to run Rosetta@home, which assembles possible proteins and searches for the lowest-energy structure of those proteins.

"It's something a 10-year-old child could use," said Baker of the software.

Rosetta@home has taken part in the biannual Critical Assessment of Structure Prediction (CASP) experiments, where predictors attempt to calculate structures that have been determined but not yet published. Predictions made by Rosetta@home of native structures for certain CASP targets began to be released this month. The prediction for target T0299, a Streptococcus protein, was very accurate. Baker believes small breakthroughs like this will eventually solve long-standing scientific problems.

BOINC is not implemented only by the Rosetta@home project. Many scientific endeavors, such as SETI@home, Climateprediction.net and World Community Grid, use BOINC to harvest processing power from science-conscious computer owners.

By employing thousands of host computers "more than 185,000 at last count --- Rosetta@home can hunt for low-energy proteins with a server that Baker asserts is comparable to some of the world's largest super-computers in terms of computing power.

UW's Housing and Food Services is working to inform students of and encourage enthusiasm for the Rosetta@home project. Ethan Owens of HFS met with RAs and provided each dorm with a Rosetta@home installation disk so students may run the programs on their computers at school.

"There is virtually no downside to running Rosetta@home on your computer," Owens said. "There's no reason for students not to install the program."

Rosetta@home is also a competitive community for some participants. Credit is given to users based on the amount of structures produced by a computer. Teams can compete to amass the most credit, or simply for the honor of discovering the lowest-energy structure.

It is easy for any UW student to contribute to the Rosetta@home project.

To download the BOINC client, visit http://boinc.bakerlab.org/rosetta and click on "Download, install, and run BOINC."

When asked to set up a project by the BOINC Project Manager, copy http://boinc.bakerlab.org/rosetta into the "Project URL" field.

BOINC will run on your computer when it is not in use, including when left on overnight or when the screensaver is activated.