ORNL invention unravels mystery of protein folding | Hacker News Reader

ORNL invention unravels mystery of protein folding

ornl.gov

26 pointsmassim13 comments

URL of their paper in PLoS ONE: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjourna...

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

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?

My knowledge of protein folding algorithms is pretty limited, and in any case everything in this press release is pretty vague.

However, this press release is dated September 14, and this is the first I'm hearing about it. A google news search for "Oak Ridge protein folding" shows only a teensy bit of small-time coverage (i.e. reprinting of the press release).

I'm inclined to think that if there was a big deal here, somebody knowledgeable would be making more noise about it.

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.

This paper is describing a way of analysing the output of molecular dynamics simulations of proteins, a series of 'snapshots' of the positions of the atoms in the protein over time.

Given the number of atoms in the molecule and the short time steps used, it's useful to be able to identify which parts of the protein (and when) in the simulation are doing something interesting and separate those from the random to-ing and fro-ing that you'd expect to occur as thousands of atoms move about. That's what this paper is describing.

It's not being applied to experimental data, and is one of many techniques used to analyse MD trajectories. I'm not an expert in these methods to assess how novel or useful this paper is compared to the others, but I would not expect that it's of interest to a layman.

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

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.

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!

Public institutions generate revenue from patents as well. All in all not a bad system as long as the revenue flows to more research. A cut is taken along the way usually so that private business expertise can help the sales & marketing process.

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

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.

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.

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