

ORNL invention unravels mystery of protein folding  - massim
http://www.ornl.gov/info/press_releases/get_press_release.cfm?ReleaseNumber=mr20110914-00

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troymc
URL of their paper in PLoS ONE:
[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjourna...](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015827)

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nickpinkston
Great to see PLoS ONE getting awesome papers! Here's to opening of academia.

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mynegation
Short URL to the patent at USPTO: <http://1.usa.gov/plfTg3>

I am not a specialist in protein folding, so take it with a grain of salt, but
from the figures it does not look like method predicts actual configurations
decoded from experiments. Patent itself acknowledges that (5.50): "the lack of
computational prediction [...] can be attributed to problems arising form
calculating molecular mechanics potentials (force-fields)".

Could anybody knowledgeable make an assessment how important this invention
is?

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jonmc12
I'm no expert, but I have explored his problem in the past as I understand
that protein folding simulations are considered by some to be the constraint
of biological life extension. Protein folding is an intractable N-body
simulation problem that relies on number of different methods to approximate
the 3D state of the protein throughout its folding sequence.

In reviewing the patent, it looks like this is an incremental improvement to
simulation based off some findings in recent years, but does not seem to be
any kind of breakthrough in understanding of proteins. Something called
'Vibration Mode' seems to be an empirical observation that explains how the
internal dynamic of the protein can limit the number of future 3D states based
on a previously observed folding cycle, and a model of the local energy minima
and maxima.

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robryan
Pretty low on detail, such as how dies this differ from the old method and
what makes it so much more efficient exactly.

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hugh3
Yeah, I was expecting at least some kind of handwaving explanation.

Usually the writing of these press releases goes like this:

1\. Researcher discovers something that's pretty cool, and as the publication
or patent is getting released decides to contact the institution's media
department

2\. Media department, if convinced that it's interesting (or just happens to
be bored) sends someone around to talk to the researcher

3\. Researcher explains what the hell the research is about to the media guy,
who then goes away and writes down some of the fraction of the conversation he
thought he understood. He collects a couple of quotes on the "Why this is
important" bit. If the researcher is lucky, he gets a draft to correct before
it goes out.

Judging by this particular press release, I can only assume that the guy the
media department sent around to the researcher's office didn't understand a
word of what the researcher was trying to say.

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smoyer
Why is there a patent on an algorithm that was developed using tax-payer
money? Or maybe more importantly, why is it "available for licensing".
Technically, I already own a small portion of the technique!

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carbocation
The Bayh-Dole Act is the reason that this can happen when the research is
federally funded (in the US).

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nickpinkston
For sure - this horrible act is poison to progress in the sciences, and I
believe has shown to be part of why medicine & med devices are so expensive.

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barbazfoobuzz
talk about deceptive titles. i know this much: protein folding is to many the
holy grail of biotech. because most(?) of the most successful biologics have
been large proteins. because protein folding is so obscure, manufacturing
large, complex proteins is non-trivial, difficult to scale up and to
troubleshoot. (using computer buzzwords since this is hn.) there are a limited
number of facilities in the world that can do it right. a delicate process to
say the least.

a more accurate headline might be: patent granted to ornl for work on protein
folding.

