Quantum Leap in Protein Folding

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jdickherber

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Message 27723 - Posted: 20 Sep 2006, 16:44:06 UTC
Last modified: 20 Sep 2006, 16:44:26 UTC

I'm curious if the scientists (or anyone else) here have any thoughts about this article:

http://www.sciencedaily.com/releases/2006/09/060918202123.htm

"As a result, they expect to streamline protein folding calculations from trillions of steps to hundreds."
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Message 27910 - Posted: 21 Sep 2006, 3:46:13 UTC

J welcome to Rosetta!

You've nailed it. THAT is why we're here. You see it's that little "they" expect to streamline protein folding phrase... that "they" is scientists such as those running Rosetta@home. "they" are using what they learn here to make predictions about proteins. Predictions that are BOTH better match to the actual protein, AND to arrive at the prediction faster. I for one am hopeful that in your childrens' lifetimes people will look back at the olden days when we USED to think the problem was difficult. And also hopeful that cures for specific diseases are found within the next decade that help the general public realize the significance of the science being done here.
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Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/
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David Baker
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Message 28148 - Posted: 22 Sep 2006, 5:59:17 UTC - in response to Message 27723.  

I'm curious if the scientists (or anyone else) here have any thoughts about this article:

http://www.sciencedaily.com/releases/2006/09/060918202123.htm

"As a result, they expect to streamline protein folding calculations from trillions of steps to hundreds."



It certainly is an interesting claim, but I haven't yet seen the paper so cannot really assess it.
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Profile Hoelder1in
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Message 28149 - Posted: 22 Sep 2006, 6:49:55 UTC - in response to Message 28148.  
Last modified: 22 Sep 2006, 6:50:21 UTC

I'm curious if the scientists (or anyone else) here have any thoughts about this article:

http://www.sciencedaily.com/releases/2006/09/060918202123.htm

"As a result, they expect to streamline protein folding calculations from trillions of steps to hundreds."



It certainly is an interesting claim, but I haven't yet seen the paper so cannot really assess it.
Here is a link to the full text of a relatively current paper by the same author, titled "Dominant pathways in protein folding", so presumably it is about the same method as the paper in question:

http://arxiv.org/pdf/q-bio/0510045
Team betterhumans.com - discuss and celebrate the future - hoelder1in.org
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Message 28157 - Posted: 22 Sep 2006, 7:45:50 UTC

A quantum leap/jump is the smallest amount anything can move. I frequently see the term "quantum leap" used and wonder if the author really understands what s/he has written!
Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.
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Message 28160 - Posted: 22 Sep 2006, 8:26:10 UTC
Last modified: 22 Sep 2006, 8:30:55 UTC

It seems they are describing the actual folding process and how it happens according to the rules of physics. That is more what folding@home is doing - simulating the whole folding process of a protein. However they claim to reach the final, native structure with very few steps. I wonder if one can develop an algorithm for Rosetta based on their work, but I doubt.

I participated in programmers dicussions about chess engines and know that most scientific papers of computer chess were of little worth for real engines because e.g. the claims of reducing the search space relied heavily on the actual engine used in the experiment and are most of the time not applicable to other engines. So it might well be that the reduction of steps achieved by Pederiva et al. are relative to just a random search and would not speed up Rosetta (which already uses some kind of restriction of the search space iirc).

Ah, here is the snag:

"Simulations using more sophisticated all-atom models are in progress and will
clarify whether these are general features or are biases of the topology-based model adopted in this work."

edit: In the paper Hoelderl1n linked to they studied one tiny protein, with just 36 amino acids. Whether there findings work for other proteins is not clear.
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Message 28240 - Posted: 23 Sep 2006, 8:26:16 UTC - in response to Message 28157.  

[quote]A quantum leap/jump is the smallest amount anything can move. I frequently see the term "quantum leap" used and wonder if the author really understands what s/he has written![/quote

Quantum leap is understood to be a 'step change' in the broadest sense.... navel staring does not change anything.......thus take language and learn the 'meaning' of the word.....

it's magnificent if there is someone thru all the trillions of trial and error calculations and discovered to recognise the shortest path to the correct result. Only by sharing new visions and theories, can new steps be developed and trialed.
Coelum Non Animum Mutant, Qui Trans Mare Currunt
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Message 28356 - Posted: 24 Sep 2006, 16:34:22 UTC
Last modified: 24 Sep 2006, 16:51:08 UTC

Quantum leap is understood to be a 'step change' in the broadest sense.... navel staring does not change anything.......thus take language and learn the 'meaning' of the word.....

Quantum leap is certainly a step change, but "a quantum leap", singular, is the smallest change possible is a system, look it up. It may be "understood to mean other things", but the people doing the "understanding" clearly do not understand the physics.

Accepting the abuse of the terminology is how problems start, it should be corrected - that is science.
Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.
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SekeRob

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Message 28542 - Posted: 26 Sep 2006, 13:03:25 UTC - in response to Message 28356.  

Quantum leap is understood to be a 'step change' in the broadest sense.... navel staring does not change anything.......thus take language and learn the 'meaning' of the word.....

Quantum leap is certainly a step change, but "a quantum leap", singular, is the smallest change possible is a system, look it up. It may be "understood to mean other things", but the people doing the "understanding" clearly do not understand the physics.

Accepting the abuse of the terminology is how problems start, it should be corrected - that is science.


your sig says it all!

Coelum Non Animum Mutant, Qui Trans Mare Currunt
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Message boards : Rosetta@home Science : Quantum Leap in Protein Folding



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