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Folding@Home - Yet Another Distributed Client
braind writes: "The Stanford group has developed a new way to simulate protein folding ("distributed dynamics") which should remove the previous barriers to simulating protein folding. However, this method is extremely computationally demanding and we need your help.
You can read more on the site." It's interesting seeing all these projects coming out - just a reminder that distributed is still around and we can always use more on our team. *grin* [addendum from timothy:] Note that the SDK used for this project was discussed here a few days ago, so you can even roll -- err, fold -- your own.
(1) proteins are not static structures, they tend to change conformations in response to stimuli like binding to a ligand, or changes in the electrostatic microenvironment around them.
(2) many proteins don't like to fold in isolation, they require the presence of other proteins that they naturally interact with.
(3) protein sequence is linear (so-called primary structure); while local structural details may be predictable with some reliability (the so-called secondary structure, things like alpha helices and beta sheets), ultimately it is the final 3D fold with long range interactions (tertiary and higher structures) that form the final structure. You can imagine that the longer the protein, the harder it is to fold, due to the increased number of potential tertiary interactions.
determination of the structure of a protein, and even relatively large protein complexes is not as technically challenging as it used to be for biophysicists these days. Tom Steitz's group at Yale has managed to crystalize and solve the structure of the large ribosomal subunit (a **HUGE** molecule as far as the average biological molecular complex goes) at 2.4 angstrom resolution, which in itself is a monumental feat. I would not be surprised if Steitz is in contention for the Nobel prize for this work.
The holy grail is eventually being able to reverse engineer a protein or ligand that is able to bind to part of a particular protein, using rational design. This is much harder than solving a structure. Pharmaceutical companies would love to be able to design this type of molecule for use as designer drugs, since it would take away much of the cost of R&D through trial and error. Big companies such as Merck basically screen for drugs the way Thomas Edison used to test materials; by having a warehouse full of stuff and testing it all.
That being said, it's still a cool project :)
NO CARRIER
Umm, I'd suspect they are likely to follow in the footsteps of a lot of the "dot-com"s. While some will argue "it sounds good on paper", that's where it should stay. I won't bore you with the details. But, this won't scale and simply cannot work without a great deal of costly planning and infrastructure which is ultimately unprofitable. But then, who cares about profitable *smirk*
Just think about it... you owe how many people three cents? Is that 0.03$US or 0.03$CDN? What about the inscrupulous people SETI and DCTI already have to deal with? These problems (and many others) aren't simple and a handful of MBA's with fists full of seed-money aren't competent to deal with them.
Most of the clones are the ideas of business types. They have little or no computer science or engineering background. To these people, all numbers are preceeded by a dollar sign. Most of them point to SETI as the basis for their business: SETI has zillions of... blah, blah, freakin' blah. They don't understand what SETI is, how it works, or why thousands of people contribute entire offices of machines to the cause. They see that big number and want to plant a `$'!
A few years ago everyone wanted to be an ISP. A year ago everyone wanted to be a "dot-com". A few months ago everyone was chanting IPO -- Redhat stock is where now? Now everyone wants to be an "ASP" and "distributed network"s are all the rage. (Technically, they are all client-server not distributed. They form an easily splintered tree; the clients do not talk to each other. However, like profitability, no one cares.)
A few years ago I worked in computational chemistry for a pharmaceutical company. Determining the conformation of a molecule is a *hard* problem. We're dealing with quantum mechanics (QM) rather than classical mechanics and many-body QM problems are notoriously difficult. For example if you have just *two* particles the space of possible configurations is 6 dimensional (in this simple example you can use symmetry to simplify things). The wavefunction is a function on a six dimensional space. For a protein you might want to deal with hundreds or thousands of nuclei and many more electrons. You might be determining a wavefunction on a 100,000 dimensional space. Let me give a taste of how big that is. Imagine we discretise this space so that we only have *ten* steps along each dimension. Then we have 1 with 100,000 zeros after it discrete points in the space. That's *big*. So clearly any attempt to solve this problem on a classical (ie. non-quantum) computer is a gross approximation. I have serious doubts about our ability to solve this problem today - even with a billionfold increase in the power of computers. When I worked in this computational chemistry department all of the molecular modelling packages had parameters you could tune. A computational chemist would run a simulation. If the result wasn't to their taste they'd tweak the parameters and run it again. Then they'd run it a few more times. As X-ray data came in they'd fine tune their parameters to make their simulated model match. Eventually they'd give a seminar showing how their simulation matched the real results - when in fact all they'd done is find the set of simulation parameters that matched reality. These parameters were purely hacks tweaked to make things look like the experimental results. They had no a priori worth. If you took these tweaked parameters and tried them on the next simulation with a different parameter guess what! They wouldn't work. And this was for relatively simple biologicaly active compounds - not entire proteins. This is a problem that grows exponentially with the number of bodies. Thankfully some of these people realised that what they were doing was no better than Voodoo. So I hope someone can convince me that there have been big improvements before we collectively build the world's biggest waster of CPU time. Keep your cycles for SETI@home - at least then they might be useful.
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-- SIGFPE
> I hope they come out with a version that can work without the screensaver.
yea, you're not alone and we do have one (for linux and windows): check out the Folding@home site and go to the download page, sign up, and then download.