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Folding@home - Distributed.net for protein

By theboz in MLP
Wed Dec 20, 2000 at 01:30:57 PM EST
Tags: Science (all tags)
Science

Here's a link I was given earlier for a distributed computing project that will help scientists understand proteins and how they are folded called folding@home.

I had been looking for something more interesting than proving something already known like distributed.net, and something that could be more immediately helpful and less abstract than seti@home. I think this is it. What do you think?


Here is a section taken directly from their FAQ to help explain the project:

Understanding how proteins self-assemble ("protein folding") is a holy grail of modern molecular biophysics. What makes it such a great challenge is its complexity, which renders simulations of folding extremely computationally demanding and difficult to understand. (See Scientific Background for more details about what are proteins, why do they fold, why this is so difficult, and why do we care).

Our 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 (see below). We have already demonstrated that our distributed dynamics technique can fold small protein fragments and protein-like synthetic polymers. The next step is to apply these methods to larger, considerably more important and complicated proteins. Unfortunately, larger proteins fold slower and thus we need more computers to simulate their folding. While the alpha helix folds in 100 nanoseconds, proteins just a little larger fold 100x slower (10 microseconds). Thus, while 10-100 processors were enough to simulate the helix, we will need many more to simulate these larger, more interesting proteins.

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Poll
What is your favorite distributed project?
o Distributed.Net 16%
o Seti@Home 26%
o Folding@home 4%
o Your mom 35%
o Napster 16%

Votes: 42
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Related Links
o folding@ho me
o Also by theboz


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Folding@home - Distributed.net for protein | 2 comments (2 topical, editorial, 0 hidden)
Protein Folding (4.00 / 1) (#1)
by Mad Hughagi on Wed Dec 20, 2000 at 03:37:17 PM EST

One of the professors at my university does quite a bit of work on writing simulations of this exact nature, although we don't have the iron to do more than simple problems in our department. This area of research has really become quite popular of late, and the computing resources are in very high demand.

It really does have quite a fair deal of significance in todays bio-tech crazed world, and the end results of the research are extremely important to humanity not only on an intellectual "need to know it for the sake of it basis"", but on the basis of fighting disease and health problems as well. Want to have that warm fuzzy feeling that you're helping to do something good each day? Load this up and maybe you're contribute to making the world a better place.

I'm not too familiar with their method for distributing the data and crunching the numbers, but if it is fairly easy to use I would definately recommend this to anyone with a decent connection. I'll probably check it out when I get back to university land...


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Citations (none / 0) (#2)
by sydney094 on Wed Dec 20, 2000 at 08:37:28 PM EST

are always nice. My major problem with this project is that they haven't released their algorithm yet. Protein folding is not as simple as running a cryptographic cracking scheme. Each calculation is based upon the values of the prior calculation. Without a good management scheme it is not very efficient to have too many nodes of a distributed network working on one protein.

Folding in an ab initio approach is not the best approach due to the massive amounts of permutations required. This is the approach of most distributed cracking algorithms.

This leaves us with an algorithm that is somewhat smarter. Kinda like a back-tracking algorithm. However, each step requires a lot of computations, and each next step depends on its parent. This might be a good candidate for a distibuted project if there were unlimited folding parameters, but unfortunately, there is a relatively small number of possible conformations that an amino acid can take.

This might end up working out well, but it should be looked at with skepicism until they publish their algorithm. And even then, it should also be noted that even the most advanced algorithms pale in comparison to x-ray crystallography in terms of accuracy and time. True, not every protein lends itself to the cryo process necessary for a good x-ray scatter, but it is still more accurate and will be used to verify any results that the Folding @ home project comes up with.
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Folding@home - Distributed.net for protein | 2 comments (2 topical, 0 editorial, 0 hidden)
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