Folding @ Home

[filthy]

I was getting 6400+PPD with my GTX 260 Core 216 Superclocked. I just got another one after a $180 off sale and can't wait to run em both.

Whenever Arctic Cooling gets the coolers for these puppies out, the PPD is going up! lol.
Said they were supposedly out in March, but April 2nd and still no show.

[mboy67]

PPD on a single system depends on what's inside.
my one box with a AMD tri core CPU and 3 9800GT's gets 13000 average but that changes with different projects, the others very as well .

[Cruel_Intentions]

I know PPD is heavily dependant on the components, I was just wondering what others were getting

[mboy67]

The science behind Folding@home


What are proteins?

Proteins are necklaces of amino acids --- long chain molecules. Proteins are the basis of how biology gets things done. As enzymes, they are the driving force behind all of the biochemical reactions which make biology work. As structural elements, they are the main constituent of our bones, muscles, hair, skin and blood vessels. As antibodies, they recognize invading elements and allow the immune system to get rid of the unwanted invaders. For these reasons, scientists have sequenced the human genome -- the blueprint for all of the proteins in biology -- but how can we understand what these proteins do and how they work?


Why do proteins "fold"?

However, only knowing this sequence tells us little about what the protein does and how it does it. In order to carry out their function (eg as enzymes or antibodies), they must take on a particular shape, also known as a "fold." Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called "folding." One of our project goals is to simulate protein folding in order to understand how proteins fold so quickly and reliably, and to learn about what happens when this process goes awry (when proteins misfold).


Protein folding and disease: BSE (Mad Cow), Alzheimer's, Huntington's, ...

What happens if proteins don't fold correctly? Diseases such as Alzheimer's disease, cystic fibrosis, BSE (Mad Cow disease), an inherited form of emphysema, and even many cancers are believed to result from protein misfolding. When proteins misfold, they can clump together ("aggregate"). These clumps can often gather in the brain, where they are believed to cause the symptoms of Mad Cow or Alzheimer's 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!


Our solution: Use new distributed computing algorithms to simulate what wouldn't be possible before

Our group has developed multiple new ways to simulate protein folding which can break the fundamental barrier of simulating experimental timescales by dividing the work between multiple processors in a new way -- with a near linear speed up in the number of processors. Thus, with power of Folding@Home (over 100,000 processors), we have successfully smashed the microsecond barrier, simulating milliseconds of folding time and helped to unlock the mystery of how proteins fold.


What have we done so far and where are we going?

Folding@Home has been a success. In 2000-2001, we have folded several small, fast folding proteins, with experimental validation of our method. We are now working to further develop our method, and to apply it to more complex and interesting proteins and protein folding and misfolding questions. Since then (2002-2006), Folding@Home has studied more complex proteins, reporting on the folding of many proteins on the microsecond timescale, including BBA5, the villin headpiece, Trp Cage, among others.

More recently (2006-present), we have been putting a great deal of effort into studying proteins relevant for diseases, such as Alzheimer's and Hunntington's Disease. You can learn more about our results and peer-reviewed scientific achievements on our Papers Page.


How can I learn more about how Folding@home works and what Folding@home has done so far?

A good place to start to learn about some of our success with Folding@Home as well as how Folding@Home works is with some of our recent papers or recent press accounts of our work. Also, please check out our FAQ and in particular, our page on the diseases and biomedical questions we are studying.