The Mother Board

Our goal: to understand protein folding, protein aggregation, and related diseases

What are proteins and why do they "fold"? Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out their biochemical function, they remarkably assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, remains a mystery. Moreover, perhaps not surprisingly, when proteins do not fold correctly (i.e. "misfold"), there can be serious effects, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, and Parkinson's disease.

What does Folding@Home do? Folding@Home is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. We use novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously achieved. This has allowed us to simulate folding for the first time, and to now direct our approach to examine folding related disease.

WHY IS PROTEIN FOLDING SO DIFFICULT TO UNDERSTAND?

It's amazing that not only do proteins self-assemble -- fold -- but they do so amazingly quickly: some as fast as a millionth of a second. While this time is very fast on a person's timescale, it's remarkably long for computers to simulate.

In fact, it takes about a day to simulate a nanosecond (1/1,000,000,000 of a second). Unfortunately, proteins fold on the tens of microsecond timescale (10,000 nanoseconds). Thus, it would take 10,000 CPU days to simulate folding -- i.e. it would take 30 CPU years! That's a long time to wait for one result!



A SOLUTION: DISTRIBUTED DYNAMICS


To solve the protein folding problem, we need to break the microsecond barrier. Our group has developed a new way to simulate protein folding which can break the microsecond barrier by dividing the work between multiple processors in a new way -- with a near linear speed up in the number of processors. Thus, with 1000 processors, we can break the microsecond barrier and help unlock the mystery of how proteins fold.