Difference F@H and R@H???

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Niehaus
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Message 668 - Posted: 26 Feb 2006, 2:54:08 UTC

Hi,

i have been looking on their pages but i wasnt able to figure out what the differences are.

Seems to me that both have same aims...
isnt it a waste to do this in 2 seperate projects?
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Aaron Finney

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Message 670 - Posted: 26 Feb 2006, 3:59:39 UTC - in response to Message 668.  
Last modified: 26 Feb 2006, 4:01:04 UTC

Hi,

i have been looking on their pages but i wasnt able to figure out what the differences are.

Seems to me that both have same aims...
isnt it a waste to do this in 2 seperate projects?


They are similar in nature in that they both have to do with protein structure, but attack different areas of the problem.

Also - This is the ALPHA Test project for Rosetta@Home. These types of questions are better asked on the Rosetta@Home message boards, found at that project\'s site located at http://boinc.bakerlab.org/rosetta/
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Niehaus
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Message 682 - Posted: 26 Feb 2006, 16:15:45 UTC
Last modified: 26 Feb 2006, 16:27:20 UTC

they are not just the same in nature but they do EXACTLY the same!

They predict how Prots fold...or do they use different algorithms?

a dumb waste of computing time...
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Profile UBT - Halifax--lad

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Message 684 - Posted: 26 Feb 2006, 18:45:09 UTC - in response to Message 682.  

they are not just the same in nature but they do EXACTLY the same!

They predict how Prots fold...or do they use different algorithms?

a dumb waste of computing time...


They do no where near the same, go over to Rosetta and read the forums all the info is there

Join us in Chat (see the forum) Click the Sig


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Spare_Cycles

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Message 685 - Posted: 26 Feb 2006, 18:53:00 UTC - in response to Message 682.  

a dumb waste of computing time...

I smell a troll.
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Niehaus
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Message 686 - Posted: 26 Feb 2006, 19:18:10 UTC
Last modified: 26 Feb 2006, 19:27:59 UTC

hehe
I just hear that they are so different, but no-one is able to explain the difference...
(because there is none...???)


BTW, what u mean by troll?
hey i\'m a noob
but i\'m interested!
i was just looking for answers, didnt want to critizie the project!

it would be nice if someone could explain it, instead of saying look there and there...
i checked the pages but couldnt find a difference...
wouldnt it be better to share the workload of both projects to one comunity, as they both have the same aim (prediction of prot-folds). And dont tell me they dont! you can read it from their Websites!
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Message 687 - Posted: 26 Feb 2006, 21:38:53 UTC

F@H uses a low-level but physically accruate method to simulate the folding of a protein. This requires a huge amount of CPU time, like 10,000 WUs for a fast-folding protein. Because it\'s physically accurate, it gives a good idea of how the protein actually goes about folding.

It is easy to get the sequence of a protein, but hard to find it\'s structure. With the F@H method it is possible to deduce the structure from the sequence, but only for fast-folding proteins. For most proteins of interest, the F@H method is too slow.

Rosetta tries to use a higher-level approach to fold the protein. This is potentially much faster. Instead of taking 10,000 WUs for a single fold, rosetta can do maybe 100 folds in a single WU. The trouble is, the answer rosetta gets isn\'t all that great. Rosetta could get a much better answer with some more work on the algorithm. That will take a fair amount of CPU power, though, as many ideas will need to be tested under a number of conditions.

And that is what rosetta is about. We provide the CPU power, and the development team uses this power to improve the algorithm.
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Message 689 - Posted: 27 Feb 2006, 0:23:38 UTC
Last modified: 27 Feb 2006, 0:30:57 UTC

Thanks!

I think i have now understood what the difference is:


\"
Rosetta: Faster but less accurate(Bakers analogy sounds to me like he uses kind of brute-force-like methods as used in passwordcrackers); still in development to get more precise answers without losing the speed-advantage, basing on Bakers & team development

F@H, much much slower, but precise enough to do research with it, based on GROMACS
\"


Is this right?

I still think it would be a nice idea to implement F@H in BOINC.
Or is it already?
-
And what means troll?
My English is horrible, sorry...
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Message 690 - Posted: 27 Feb 2006, 0:52:41 UTC

FAH-Boinc has been under development for almost a year and still not ready. They won\'t say anything other than \"you\'ll know when it\'s ready\". It\'s not a subject their moderators will even entertain.
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Message 696 - Posted: 27 Feb 2006, 7:13:37 UTC
Last modified: 27 Feb 2006, 7:14:53 UTC

Thanks!

I think i have now understood what the difference is:


\"
Rosetta: Faster but less accurate(Bakers analogy sounds to me like he uses kind of brute-force-like methods as used in passwordcrackers); still in development to get more precise answers without losing the speed-advantage, basing on Bakers & team development

F@H, much much slower, but precise enough to do research with it, based on GROMACS
\"


Is this right?

I still think it would be a nice idea to implement F@H in BOINC.
Or is it already?
-
And what means troll?
My English is horrible, sorry...


A troll is someone that posts a message to get attention.

You were inadvertatly seen as a troll because you are in RAPLH@Home not Rosetta@Home. RALPH@Home is a place to try to get rid of bugs for Rosetta@Home before releasing it to the Rosetta@Home participants, so that the participants of Rosetta@Home do not have errors when they do the real work of folding proteins.

Your English is good enough to pass as a troll, and I can tell you that\'s pretty good English.

Edit to fix bbcode
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Dimitris Hatzopoulos

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Message 698 - Posted: 27 Feb 2006, 7:39:06 UTC - in response to Message 687.  
Last modified: 27 Feb 2006, 7:44:40 UTC

F@H uses a low-level but physically accruate method to simulate the folding of a protein. This requires a huge amount of CPU time, like 10,000 WUs for a fast-folding protein. Because it\'s physically accurate, it gives a good idea of how the protein actually goes about folding.

It is easy to get the sequence of a protein, but hard to find it\'s structure. With the F@H method it is possible to deduce the structure from the sequence, but only for fast-folding proteins. For most proteins of interest, the F@H method is too slow.


We don\'t know how accurate the F@H method is. Has F@H taken part in any CASP? Not AFAIK. For other projects we have an idea about accuracy.

Based on the info I\'ve managed to gather on F@H, I\'d say the F@H project is computing \"pathways\", frame by frame like a Pixar movie \"Toy Story\", aiming to understand the folding process itself, misfolding diseases (Alzheimer, MadCow) and perhaps create a better model of the process. I\'m not quite sure about its medical relevance.

For diffs between protein projects, have a look at the protein project diffs. And please let me know if there are any facts missing.
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Message 720 - Posted: 28 Feb 2006, 5:03:47 UTC
Last modified: 28 Feb 2006, 5:05:26 UTC

More information is here Rosetta@Home FAQ .

Edit: changed wording
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Nuadormrac
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Message 869 - Posted: 13 Mar 2006, 12:33:41 UTC

There are some differences, which were also posted at the ProteinPredictor board, comparing it to both folding@home, as well as to rosseta@home... BTW, as my credits might indicate, I was on Predictor@home longer, but also joined up with Rosseta, not long after it was released... The view there when people asked, as that the work done here (well on the parent project, not the alpha of course) is complementary, and it\'s of value to crunch for both...

As to folding, I have crunched for them in the past; however I\'m now using BOINC. If they want to get me to consider crunching there again, then they\'ll need to get the BOINC client out. Though there is a way to split CPU time between both apps (by throttling the f@h CPU time back, so BOINC gets some CPU time also); it\'s easier to just allow the BOINC CC to task switch between projects, especially as more and more projects are setup to run in BOINC.

/me just not as interested in a stand alone client anymore...
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