UW Today

This is an archived article.

January 19, 2005

UW’s Rosetta software to unlock secrets of many human proteins

University of Washington TechTransfer recently licensed software that will give scientists a huge advantage in the fight against disease.

The software, known as Rosetta, predicts how proteins fold, information that is highly valuable to biological and biomedical researchers.

UW Tech Transfer’s Digital Ventures licensed Rosetta software without charge to the Institute for Systems Biology (ISB), a non-profit research organization. The institute has partnered with IBM and United Devices, an Austin-based company, to create the Human Proteome Folding Project, a global effort to determine the structures of the approximately 60 percent of human proteins with no known function.

“How proteins fold determines how they are structured,” said Lars Malmstroem of the UW laboratory that developed the program, “And how they are structured is related to their function in the body.”

Because there is an astronomical number of possible conformations for a given protein, collecting the data would take many thousands of lifetimes to complete with conventional computers, said Dr. Richard Bonneau, one of the researchers.

But by summoning the computing power of millions of volunteers around the world, he said, the task will be completed in less than a year.

IBM’s World Community Grid, which was built using grid technology developed by United Devices, will enable millions of people to volunteer their personal computers to run Rosetta during periods of computer downtime.

The information will be entered into a publicly accessible database, which scientists can then use to conduct research into new drugs and treatments.

Rosetta works by virtually folding protein sequences into thousands of possible shapes, based on certain protein folding “rules” known by scientists. These rules are summarized in the program and are termed the “Rosetta score.” The program tries a great many conformations and returns those with the lowest Rosetta scores; these conformations come closest to the actual shape of the protein.

Rosetta was developed in the laboratory of UW Professor David Baker by a large team of scientists and students. Former post-doctoral fellow Richard Bonneau, who is now with the ISB, is the technical lead for the project. Rosetta software is available for licensing at: http://depts.washington.edu/ventures/UW_Technology/Licensing/.