Whether it’s the Blackberry on your bedside table or the laptop you bring to class every day, almost everyone can easily tap into technology 24-7.

But it’s what those machines are doing when you’re not using them that interests David Baker.

The biochemistry and bioengineering professor maintains a software program called Rosetta@Home that conducts research by using the processing power of idle computers.

People throughout the world have downloaded it, and are helping solve one of the most fundamental biological mysteries that could lead to finding cures for diseases: protein structure prediction.

Proteins, the framework for all living things, are linear chains made up of molecules known as amino acids. Though these chains are able to change their structure in order to carry out different functions, all proteins have one form that suits them best. In other words, each has a most favorable structure.

It’s pinning down this ideal state that troubles scientists. Proteins’ ability to take so many shapes makes it difficult for researchers to know if they’ve checked all possibilities for the most favorable structure. With the computing power of Rosetta’s 200,000 participants, Baker’s lab is able to collect data for a wide spectrum of structures.

“If the lab can simulate the proteins and how they interact with other molecules it could really speed up research,” said Ethan Owens, a Housing and Food Services (HFS) project coordinator. “It takes away the whole [idea of] everything done in a lab with microscopes.”

Owens, a graduate of the Astronomy Department, set up the program on 200 HFS employee computers in 2006. He and HFS Director, Paul Brown saw it as a good way for HFS to contribute to the UW’s research efforts, Owens said.

The program is collaborating with scientists creating vaccines and designing enzymes that don’t exist in nature for gene therapy, a process of inserting genes into cells and tissues to treat a disease.

“We’re most excited about designing new enzymes that create new catalyst functions, for example, making new types of fuel molecules,” Baker said. “New fuels or new things for destroying pesticides or nerve toxins – there are a lot of applications for new enzymes.”

The lab is also working on HIV vaccine research.

Since the proteins in HIV are constantly changing, the body can’t build immunity to the virus. Yet there are a few “Achilles heel” proteins that don’t change, Baker said. By focusing on these constant protein structures with the Rosetta program, Baker’s lab is helping researchers target the only proteins in the virus that could be immunized.

Rosetta uses BOINC software, a program created at the University of California Berkeley that allows data to transfer between personal computers and Baker’s lab. This allows HFS computers to run the program 24-7, switching Rosetta into low priority mode when it’s being used. Others choose to run the program manually by turning it on and off whenever they please.

Julie Lao, a senior, runs a similar program called Folding@Home that was created in a Stanford lab. The BOINC application allows her to run the program on her Play Station 3 (PS3) and her computer at the same time.

“The benefit to using the PS3 is that people use their computers a larger amount of the time than their PS3, allowing the PS3 more time and processing power to contribute,” Lao wrote in an e-mail.

[Reach columnist Meghan Peters at news@thedaily.washington.edu.]