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Researchers Determine Chemical Structure of HIV Capsid
adeelarshad82 writes "Researchers at the University of Illinois at Urbana-Champaign (UIUC) have determined the precise chemical structure of the HIV 'capsid,' a protein shell that protects the virus's genetic material and is a key to its virulence. The experiment involved mapping an incredible 64 million atoms to simulate the HIV capsid, pictured here. Interestingly no current HIV drugs target the HIV capsid and researchers believe that understanding the structure of the HIV capsid may hold the key to the development of new and more effective antiretroviral drugs. What makes this whole experiment even more fascinating is the use of Blue Waters, a Cray XK7 supercomputer with 3,000 Nvidia Tesla K20X GPU accelerators."
I guess all those gamers aren't useless after all. You can thank me later for my donations to Nvidia's profits. So they could research and develop this technology.
That there are numerous repeating elements in the capsid. Seems like this would be a perfect target for antibody formation. But obviously, that hasn't worked out. Be interesting to know why.
(Armchair biology is wonderfully simple, isn't it?)
Faster! Faster! Faster would be better!
We'll have +100 exaFLOP systems in five years, 100 times the performance. Major structures in cells, and complete viruses, will be modelled to the atomic level
Amazing, because that's exactly how I envisioned the HIV capsid would look, except in red and blue.
Better known as 318230.
just like a geodesic dome, thats kind of interesting
... or at least any supercomputer.
After all, 3 is the new 640.
Yeah, it's amazing how the evil bad guys had technology that was sixty years ahead of everybody else. Lemme guess, their cold-blooded space rulers gave them an R&D lab?
My God, it's Full of Source!
OUTSIDE_IP=$(dig +short my.ip @outsideip.net)
Smallpox was never cured--they just developed a vaccine for it. New vaccines continue to be developed, for example hand foot and mouth disease (2013), HPV (2006), rotavirus (1998), Lyme disease (1998), hepatitis A (1992), and the list goes on...
I've wondered along these lines in the past.
It's almost certain that the drug industry isn't deliberately withholding cures. Competition still exists between companies, and thanks to patents any novel cure would print money for the company that controlled it. It's not like they're in danger of running out of diseases to treat if they manage to cure a couple, is it?
But I think you're on to something with the pursuit of profit not being the best driving force for medical innovation. The cost of each dead end in drug research keeps going up as the easy fruit has been plucked already, so do drug companies want to put big money into high risk-reward scenarios? Or, as with Hollywood, would they prefer to tweak a few existing and proven blockbusters, pretend it's a new formula, and put more into advertising?
We've plateaued, perhaps, but the good news is that each new leap in neighboring technologies may lower the cost of research and ultimately of cures. I'm excited about the potential for other drug delivery systems such as artificial viruses or nanotechnology, for example.
They didn't need to simulate the *whole* capsid, it's homogeneous and any variations in it are unknowns, its like simulating 64 million atoms of carbon to understand graphene... completely pointless when a small number will do.
Illinois only just got its supercomputer finished, courtesy of a gift from the National Science Foundation, and now needs to justify that budget:
http://www.engadget.com/2013/03/29/blue-waters-supercomputer-now-online-24-7/
And Aids research is the 'cute puppies' justificaton, it's like climate research or other good deads, but actually their contribution to the science is nothing more than PR.
They didn't take a capsid. measure 64 million atoms and then simulate those atoms. They know what the capsid is made from, and they duplicated it up to the capacity of their supercomputer. The repeats are just a consequence of the small data they modeled from.
Next year, when they get an upgrade, they'll be modelling the same data into 128 million atoms, or 200 million atoms, to no extra benefit.
It reminds me of a Feyman story. How he used to make paints that could coat plastic. The competing company spend a fortune on an electron microscope thinking it would make them better, and instead they went out of business. All he had was a few test tubes, various acids and salts at his disposal. In the same way, this stuff has little to do with the cure for AIDs because its generates large amounts of simulated data not based on any new actual data.
But it does showcase their supercomputer.
Interestingly no current HIV drugs target the HIV capsid and researchers believe that understanding the structure of the HIV capsid may hold the key to the development of new and more effective antiretroviral drugs
Since the "discovery" of the HIV virus in the late 1980's scientists have discovered that the HIV virus has undergone several mutations
Even if there are drugs which can successfully targets the HIV capsid that have been decoded in this experiment, it does not mean that the HIV virus won't mutate again, and change their capsid sequence (or chemical formula) to foil those drugs
But all in all, the effort in sequencing the capsid is indeed a breakthrough, a step forward in understanding the nature of the bug, even if it's one type, amongst the many varieties
Muchas Gracias, Señor Edward Snowden !
Much like there's no point building weather prediction computers, since all we do is put data we already have from weather stations into them, and no point building FEM simulators for structural engineering since we already know how a single girder acts under stress.
Or... could it be that multiple simple elements can interact in ways that are not meaningfully predicted by an understanding of individual elements? NAW!
Yeah, greed is totally a modern invention brought about by The Evil Corporations. I think my eyes just rolled a full 360*.
Check out U.S. Patent Publication Nos. 20130053267 and 20120302556 (among others from the same assignee). Capsid structures, like protein structures, can be useful starting points for drug development. Ultimately, however, the goal is to find a substance that will kill the disease without killing the patient. So far, no computer graphics package has replaced the grunt work of medicinal chemistry---methyl, ethyl, butyl, futile.
It has always been about making a profit. It's just that there is more profit to be made in the US today due to a general lack of transparency of costs and a disconnect between costs and outcomes. If you can get past the paywall there is a great article in today's NY Times on part of the reason why medical care costs so much in the US.
Indeed. The AC was wrong. HIV is a blood-borne disease, not an STD. It didn't get to humans through sex, but from butchering monkeys for food - get a little infected blood on a cut and you'll catch it.
The GP is obviously an anti-government tin foil hat wearer and racist to boot. I can't figure out why so many anti-intellectuals like him are spouting off in a nerd site.
Free Martian Whores!
For various reasons NVIDIA's architecture is not optimal for bitcoin mining. But as you can see, it is quite powerful in other problem spaces.
I am very small, utmostly microscopic.
breakthroughs in AIDS research have in fact come from supercomputer modeling.
Strange we have the simple equations of gravitation, but can't solve them for even the simple general case of three interacting bodies. But we can use numerical methods on supercomputer good enough for modeling interactions of millions of gravitational bodies. Something must be wrong about your assumptions.
HIV is just too effective and appeared too suddenly.
How is it effective? It takes years to kill someone. And with treatment these days people with HIV have life spans equivalent to people with poorly controlled type II diabetes. Seems like if the evil government wanted to destroy us it would be easier to just sell us a lot of snack cakes and chocolate covered potato chips.
Are you really that surprised that a disease that transmits through the exchange of bodily fluids has spread through a society that thought that sex with anonymous strangers was acceptable behavior?
Can you please show me a real picture of the HIV virus?
You're right. HIV is not "the" cause of AIDS, but then again, not a single published paper in the history of the disease has made that claim.
HIV is "a" cause of AIDS. AIDS is defined as having a CD4 T-cell count 200 per microlitre.
Many medical conditions can cause AIDS, and HIV is only one of them.
Nobody has ever claimed that HIV is the one and only cause of AIDS.
You probably shouldn't base your position on information from the late 1980s.
Eh? HIV is not an STD? So it's safe for me not to wear condoms when I fuck all those different whores every night?
People are spending way too much money and effort to find the cure when there's a really simple way to prevent the infection. Just stop having sex with whores and faggots. Problem solved.
Have you heard of low amperage electric currents for stimulating the blood and irritating virus' imcluding HIV to leave the system? It's use was first studied by Havard and then MIT and had a 50% remission rate for HIV volunteers. Pretty recent also. I mean the story hasn't been out for more than 2 decades I think.
50% is not good enough for medical science, they want guaranteed cures with well understood results. But if the WHITE PAPERS were fucking available to us we should be able to sell it as a non-medical treatment without guaranteed results.
Fat chance advertising it though and getting any credibility in our crazy ass fascist SCIENCE ONLY PLEASE culture.
There's also sound waves that break up and disturb pathogens as well. But no sonic waves can't do that... without harming the rest of the host. Bullshit.
-not posting in AC because these two under-rated techs deserve my full pseudonymous support.
I will ignore any people flaming or trolling me for conspiracy, or quackery. Go fuck yourselves and suffer the consequences of the life you chose. But don't chose it for others by lobbying against this stuff.
the simple general case of three interacting bodies.
You scientist types are all perverts, aren't you?
The new right fascists are bilingual. They speak English and Bullshit.
Makes your eyes red just thinking about it
The new right fascists are bilingual. They speak English and Bullshit.