Jun 22, 2009 04:58 PM | 12
The human brain benefits from taking breaks, but a computer can go strong all day. So why not enlist its power in cutting-edge research while you are away reenergizing over coffee or lunch?
A new program is recruiting computers’ idle time in the fight against diseases like HIV infection and Alzheimer’s. Developed by a team at the University of Delaware, with funding from the National Science Foundation, Docking@Home joins a growing list of projects—from listening for space aliens to modeling climate change—that are tapping into the open-source system called BOINC (Berkeley Open Infrastructure for Network Computing).
“Even without large resources of supercomputers, we can do meaningful research with the help of volunteers across the Internet,” says Michela Taufer, an assistant professor of computer and information sciences at the University of Delaware. She is leading the project that aims to ramp up resources in the race for cures.
Testing the millions of potential components for a drug in a lab setting is extremely slow, expensive and error-prone. Instead, scientists typically use supercomputers in the early phases of research, relying on them to sort through the seemingly infinite combinations of promising molecules, called ligands. The choice ligands are those able to bind to, or “dock” inside of, a protein associated with a disease and either cancel out or produce a signal. Whereas HIV therapy would aim to turn off virus replication, Alzheimer's treatment would seek to activate a connection in the brain.
But access to this kind of computing power can be limited. “That problem can be solved by breaking up the search into little pieces and sending them out to volunteers to work on,” says Kevin Kreiser, a Ph.D. student at the University of Delaware and a member of the project staff. The team is now comparing model results from more than 6,000 worldwide volunteers to see that they match results in the wet lab. After the simulations are validated, the next step is to “go out and search for new drugs,” Kreiser says.
Donations of computers’ idle time could increase the speed with which potential new medicines enter the lab and, with luck, find their way to patients. “We will help scientists by narrowing down the list of potential target molecules,” Taufer says.
Someday users may be able to choose molecules and position them into target proteins themselves, through a graphical interface. This latest project, Kreiser says, aims to “harness users' intelligence to make computation happen faster.”
For now, volunteers can simply relax with coffee in hand and let their computers slave away. The project’s current screensaver, also developed by Kreiser, shows off users’ contributions to science with 3D representations of the molecular structures being manipulated. “You don’t have to sit there and work for hours on end,” Kreiser says. “Just let it run in the background. No pain.”
Image of HIV protease, one of the targets of the project's simulated molecules, by theasis via iStockPhoto.
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