Noah Johnson

Folding Proteins at Home

In what is rapidly becoming a new world of democratic computing, Noah Johnson’s three Power Macs are humming quietly away, helping Stanford University scientists solve a complex problem that, one day, may help them fight disease.

As part of a groundbreaking distributed computing experiment, Johnson and half a million other people are donating their spare computer capacity so Stanford can remotely simulate protein folding, an essential biochemical process that controls vital body functions.

The project, called Folding@home, represents a sort of ad hoc democracy because anyone with an Internet connection can join. Users simply download an application that runs protein-folding simulations on their desktop computers when the systems are idle.

Origami Gone Wrong

If you think of a cell as a house, proteins are everything that goes in it — the framing, the furniture, the fixtures. Proteins are the working parts of living matter.

The human body makes at least 50,000 different proteins, and each one assumes a particular shape, known as a “fold,” to carry out a particular function. Hemoglobin folds into a shape that lets it carry oxygen. Insulin fits like a key into spaces so it can turn things on and off. Other proteins fold into shapes that build bones, muscles, hair, skin or blood vessels.

When proteins don’t fold properly — think of origami gone wrong — they can poison the cells around them and trigger diseases such as Alzheimer’s, cystic fibrosis, an inherited form of emphysema and even many cancers.

“Folding@home pulls simulation packets from Stanford servers, makes folding calculations on the Mac and sends results to the Stanford server.”

Sharing the Workload

“Scientists have already sequenced the human genome, which is basically a blueprint for all of the proteins in biology,” says Johnson, a computer programmer who folds at home as a hobby.

But analyzing a protein’s possible folding steps as it crumples up into a 3-D knot is daunting task, even for a supercomputer, because the molecular backbone of a protein can fold in trillions of different ways. While several supercomputers used together could handle the job, time slots on supercomputers are tight and very expensive.

Through Folding@home, scientists now have the horsepower to study the mechanics of protein folding. With its ability to share the workload among hundred of thousands of computers economically, Folding@home can help scientists understand how proteins snap, or don’t, into their predestined shapes — and may help to explain the origins of diseases such as Alzheimer’s and apparently unrelated diseases.

New Algorithm

Dr. Vijay Pande, a professor of chemistry and structural biology at Stanford, saw the potential for thousands of desktop computers to calculate tiny portions of a folding sequence. He wrote algorithms for Mac, Windows and Linux computers, and worked with distributed-computing entrepreneur Adam Beberg to integrate his code into an application dubbed Folding@home.

When the application is running on a Mac or other computer, Pande’s software pulls simulation packets from Stanford servers, makes folding calculations on the Mac and reports the results back to the Stanford server.

Johnson says he “decided to get into folding because it helps research into diseases. You don’t have to be a scientist to help. You don’t have to understand complex biological molecules to make a difference.”

Processors of the World, Unite!

Folding@home isn’t the world’s first project that uses the spare capacity of thousands of computers in loosely-linked networks. The same distributed computing concept fueled the discovery of the largest prime numbers and deciphered an RC5-65 encryption algorithm.

The most famous distributed computing project, the Search for Extra-Terrestrial Intelligence (SETI@Home), uses millions of desktop computers to analyze radio telescope data in an the ongoing search for extraterrestrial life.

Since Folding@home debuted in 2000, more than 500,000 computers across the globe have helped simulate the complete folding behavior, atom by atom, of five important proteins.

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