Stanford University
Protein Researchers Bring Mac Users into the Fold
As the workhorses of the biological world, proteins can act as enzymes that drive biochemical reactions or antibodies that fight unwanted invaders. What mystifies researchers is how proteins carry out their work. One thing scientists do know: proteins self-assemble into particular shapes or “folds,” transforming themselves on the fly to accomplish an amazing array of tasks. Scientists also know that when proteins don’t fold properly the result can be diseases such as Alzheimer’s, cystic fibrosis, Mad Cow disease, and even many cancers. To better understand how proteins fold in the hopes of discovering possible cures for illnesses, Stanford University’s Pande Group is asking for help from Mac users willing to put their idle computers to work running Folding@home, a massively distributed simulation of how proteins assemble themselves.
Until now, only PC users on Windows or Linux could run the Folding@home simulation program, but now Mac users running Mac OS X can donate their computer time as well. For Dr. Vijay Pande, assistant professor of chemistry at Stanford University and principal investigator on the project, the decision to bring the Folding@home software to the Mac was easy. “Creating Mac OS X versions of our existing UNIX-based client and server software was painless and fast — a matter of a few days,” says Dr. Pande. “It was a relatively small investment in time, and we hope to get a substantial payback in return.”
Dr. Pande believes that he can attract thousands or even tens of thousands of Macintosh users connected to the Internet to run the Folding@home software. “Many Mac enthusiasts are scientists who are likely to be interested in what we’re doing,” he says.
Dr. Pande’s ultimate goal is to understand how proteins assemble themselves and what their final structure is. This is something that is difficult if not impossible to determine from experiments alone, because folding happens at an extremely rapid pace, often in a matter of microseconds. Each step of the folding process is enormously complex, and a single computer — even the world’s fastest supercomputer — can’t calculate all of the variables fast enough.
“A single Power Mac is blazingly fast, faster than the processors that make up most supercomputers.”
— Dr. Vijay Pande, Assistant Professor of Chemistry, Stanford University
Calling All Power Mac Users
Simple proteins assemble in about 10,000 nanoseconds, and one 400MHz computer can simulate 1 nanosecond of assembly time in about a day. This means 1,000 participants are needed to simulate a simple protein fold in 10 days, and that’s just for simple folds. More complex proteins can take far longer.
Dr. Pande needs a substantial amount of processing power to allow him to simulate larger, considerably more important and complicated proteins. That is why he and his associates built the Folding@home service as a distributed-computing peer-to-peer network, much like SETI@Home, distributed.net, and Gnutella. Dr. Pande used the Mithral Client-Server SDK, a software development kit specifically designed to build massively distributed applications. The server software, which for Mac volunteers runs on a PowerBook at Stanford, hands out work for the clients to do, then collects the results.
Dr. Pande is especially excited about the potential for harnessing thousands of Power Macs as clients. “A single Power Mac is blazingly fast, faster than the processors that make up most supercomputers,” he says.
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