Thread: Keep It Up!!
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Unread 07-02-2003, 01:27 PM   #21
xerka
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Join Date: Mar 2001
Location: Denver, CO
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Quote:
Can I cause the client to pop up only after 5 mins of inactivity (i.e. Can I replace the screensaver with it) ?
I would just install the client as a service, the client is set to not interfere with anything you do. On the priorty its really low so it only uses your spare cpu power. I have even run bench marks and get the same score with and without running it as a service.

Quote:
What are the similarities and differences between F@H and DF ?
Just to delve a little deeper here is what "Brian the Fist"(one of the main guys) says
To answer the question you are really asking, the difference (among other things) is that F@H attempts to fold small peptides (not big enough to be called proteins) by parallel molecular dynamics (MD). Normally MD cannot be done in parallel but they have devised a clever way to do so. Unfortunately anything big enough to resemble an actual protein is still computationally intractable with this approach. Nevertheless we can learn many things about the protein folding pathways, etc by studying how these smaller protein fragments fold.

We on the other hand, especialluy with the new beta, are looking at the folding pathways of full (albeit small) proteins. Our ultimate goal originally was to predict the final folded structure of the proteins, regardless of how we get it. However now we find that we can as a bonus also sample folding pathways at the same time to track HOW the proteins fold and this can later be compared with experiment. If they match it suggests our folding simulations may approximate reality. In order to handle much larger protein sequences than F@H, we obviously have made concessions. We do not use the 'tried and true' MD approach (which has been around for decades) but rather use an extension of our TraDES algorithm to perform a coarse-grained dynamics simulation which takes much larger steps in conformational space. It remains to be seen with the beta testing if this approach can get us to the native fold of the protein, given an ideal scoring function to guide it, but so far we have gotten close (4.5A RMSD is the record so far I believe, from the previous beta - ideally we should get 1-2A which is why we're still trying different algorithms).

If you got lost somewhere above there, you may have to do some reading on the web site to make sense of things

^Taken from this thread http://www.free-dc.org/forum/showthr...ighlight=f%40h
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