What the hell?

I'm perfectly serious.

The nerdier elements amongst you will have heard of the seti@home project. They send data, radio waves, that they collect from the cosmos to your home computer, and your computer scans the data looking for patterns or messages that alien species beam off into the cosmos. It's pretty much a waste of time that is designed to keep beardy Trekkies off the streets. But it was the first example of people pooling their CPU power for a common cause. They did it with Mersenne prime numbers as well.

But fuck all that. This is much cooler.

The rosetta@home project is similar, yet much more useful. It is exactly the same structure of project (they create data, send them to your CPU, your CPU solves it and sends it back) but it does something more handy - determining the folding structure of a protein.

So who gives a shit about protein origami? Everyone in a white coat. Proteins, like all other natural systems, tend towards their natural equilibrium, their most stable state. Unfortunately that is very hard to determine because proteins are made out of many, many amino acids all of which fold up and behave differently. When you get a string of, say, 800 amino acids to make a protein, we have literally no fucking idea how the outside of the molecule looks unless we test them.

So, what does a large brute-force numerical solution to a problem need? Yes - masses and masses of computer power. Hence, this project. Here's the stuff they're working on:

"Malaria: We are part of a collaborative project headed by Austin Burt at Imperial College in London that is one of the Gates Foundation "Grand Challenge Projects in Global Health". Malaria is caused by a parasite that spends part of its life cycle inside the mosquito, and is passed along to humans by mosquito bites. The idea behind the project is to make mosquitoes resistant to the parasite by eliminating genes required in the mosquito for the parasite to live. Our part of the project is to use our computer based design methods (ROSETTA) to engineer new enzymes that will specifically target and inactivate these genes.

Anthrax: We are using ROSETTA to help John Collier's research group at Harvard build models of anthrax toxin that should contribute to the development of treatments. You can read the abstract of a paper describing some of this work at http://www.pnas.org/cgi/content/abstract/102/45/16409.

HIV: One of the reasons that HIV is such a deadly virus is that it has evolved to trick the immune system. We are collaborating with researchers in Seattle and at the NIH to try to develop a vaccine for HIV. Our role in this project is central--we are using ROSETTA to design small proteins that display the small number of critical regions of the HIV coat protein in a way that the immune system can easily recognize and generate antibodies to. Our goal is to create small stable protein vaccines that can be made very cheaply and shipped all over the world.

Other viruses: We have been collaborating with Pam Bjorkman's laboratory at Cal Tech to use the ROSETTA protein-protein docking methodology to build models of herpes simplex virus proteins in complex with human proteins.

Alzheimer's disease: Alzheimer's and many other diseases are likely to be caused by abberant protein folding in which proteins form large aggregated structures called amyloids rather than folding up into their normal biologically active states. A big advance was made recently by David Eisenberg's research group at UCLA in solving the first structure of an amyloid. We are collaborating with their research group to use the structure to predict which parts of proteins are likely to form amyloids, which will be a first step to blocking amyloid formation and hopefully disease.

Cancer: Cancer can be caused by mutations in key genes that disrupt normal cellular control processes. We are developing methods for cutting DNA at specific sites in the genome, and we will be targeting sites that are implicated in cancer. After these sites are cut, they should be repaired by the cell using a second, unmutated copy of the gene and the cell should no longer be cancerous. This is a very specific form of gene therapy that, if successful, will circumvent one the main objections to current gene therapy methods; namely, current methods insert the unmutated copy of a gene randomly into the genome, and if the insertion point happens to be near an oncogene, the gene therapy will cure one disease but cause another. Because our methods will target specific sites instead of random sites, they should avoid this pitfall.

Prostate Cancer: The androgen receptor (AR) binds testosterone and is responsible for normal male development. When the AR becomes hypersensitive to testosterone, prostate cancer is the result. The current treatment for prostate cancer, called "hormone therapy", involves lowering the amount of testosterone available (sometimes by castration). Many malignant tumors are resistant to this therapy, however, so we are applying our protein design methodology to find different ways to inhibit the AR and to treat prostate cancer. Specifically, we are trying to design proteins that will disable the AR even in the presence of testosterone. We are doing this by designing proteins that will prevent the AR from entering the nucleus of the cell (which is where it does its dirty work), and also preventing it from binding DNA and activating tumor-specific genes even if it does get into the nucleus."

If you're anything like me, you probably leave your computer on for several hours a day while you're not around it. So make it do something useful instead of display that Cephalic Carnage screensaver over and over again. This program does absolutely nothing but work on determining the structure of a protein while you're away from your PC.

And trust me, if your computer figures out a dramatically effective way that antibodies stick to the HIV structure, and the data for the base structure for an AIDS vaccine starts in your CPU, you'll have your own special footnote in history.

"History was made today as an ugly spotty 16 year old metalhead discovered a key weakness in the human immunodeficiency virus. While he was dreaming about buying a better set of pickups and getting band groupies, his computer found an area on the virus where certain amino acids, when enzymatically bonded, would cause the body would generate normal antibodies and neutralise the virus. A vaccine is a few years away, but the discovery has the potential to save several million lives and all but eradicate AIDS from the planet. The metalhead, known only as "666slipkn0tkarnag3" could not be reached for comment but it is widely believed that somewhere he is playing power chords, chronically masturbating and unaware of the fact that he saved an entire generation of Africans."

But seriously... get the software and help. It's good for the soul.

__________________

Thats pretty cool, and a great idea. I'm all about it, because my computer is always on when I'm out getting stoned or chasing women.

(Downloads software)

__________________

that is one of the most interesting things i have read in a while. thanks FBS. so, let me get this correct, pretty much they are figuring out the amino acid structure and leaving it up to everyone elses computer to figure out how it crumples up?? THAT IS INSANE! i just dont see how that will work.....but then again, i don't think i care to either.
this kind of shit makes me want to start reading/studying biology again. i just fucking hate the chemistry aspect.

__________________

Yeah, that's close enough.

__________________

Its beautiful really

__________________

SETI

Search for Extraterestrial Intelligence also employs peoples computers at home to help sort data in the hopes of finding signals in space from intelligent life forms. They get more data than they can decode so a small prog is available for anyones home PC to lend a helping hand.

Thanks for overstating

I'm downloading it now. I'm going to be immortal GOD DAMNIT!!!!!

__________________

Thats insane

Yeah its really cool,they have the same type of program decyphering old WWII Codes, it sends them to your computer and you computer cracks it and sends it back, shame you dont get to see them.

__________________

This is awesome. Now I don't feel so bad about not being honest with all those women...

I remember SETI, it was cute. I always wanted to get it when I was younger but my computer couldn't handle it.

__________________

why would we still be decoding that stuff, completist collection of data or something? archiving?

__________________

I really wish that wasn't so long. I'll read it later.

__________________

i know someone that has the delta 32 mutation. lucky son of a bitch. very rare to find somone with the delta 32 mutation.
delta 32 makes u completely immune to aids/hiv and plague.

__________________

Am I the only one that finds it a bit amusing the the AIDS finding computer program is called BOINC?

__________________

I joined up for the Rosetta@home thing. Pretty fuckin cool idea i reckon.

And now i feel all tingly

Haha go into BOINC and select your project and show graphics... Look at the little suckers go!

__________________

That's the kind of thing that we're interested in here.

From memory, they also found a bunch of East African women several years ago who have similar or related mutations.

__________________

LOL

__________________

thats exactly what i was talking about. just i was referncing the plague incident.

__________________

Is he related to Andy Collyer?

hmm?

Oh deary me. FBS, good for the soul? Come on, don't let me down like this. But, at least I find it reassuring that you didn't mention yourself as the potential "discoverer". There is a limit to how many times the word, with variations, "FUCK" can be accepted in a respectable foot note of history.

And to all of you who have choosen to let your computers work on the defeat of AIDS, welcome aboard.
To the rest of you - take the time, download the software. It's good for your sex life.

__________________