Quick Jump Daily Digest

**Jammie** · 04-13-2006, 11:35 AM

I was thinking that it would be good to start a QJ.Net Folding@Home Team. Now before you say no, watch this video. Pretty moving, isn't it? (well it moved me).

Folding@home is a distributed computing program (like SETI@Home, except Folding@home has actually found out things, unlike SETI@Home). It's pretty easy to set up, and it only uses your computers processing power when you're not ojn you PC. So what do you say? If a few people are willing to join I'll create the team.

EDIT: The team page is located here

**Chrono6456** · 04-13-2006, 11:45 AM

Looked awsome, Ill join ^_^

**Jammie** · 04-13-2006, 11:46 AM

OK, I'll create the team. How does "Team QJ.NET" sound for a team name?

**Josey Wales** · 04-13-2006, 11:50 AM

I dont get it. I dont get how downloading a program has anything to do with the proteins in the human body...

**Jammie** · 04-13-2006, 11:54 AM

It simulates how they form. The proper term is how they fold. If we know how they fold, we can unfold them, and by them I mean cancer, etc.

EDIT: The team is number 50073 and our homepage is here

**Josey Wales** · 04-13-2006, 11:57 AM

Im sorry. Im still completely lost. The idea is that, proteins in the body "fold" and when they do it wrongly you get dieseases or something, right? So how does running a program on your computer has anything to do with simulating the way real proteins work? Im just missing the logic and principle behind this whole project...

**Jammie** · 04-13-2006, 12:01 PM

Yes, when the fold incorrectly you get diseases. Your computer is given a packet of data and simulates how it could fold. Also there are other people who get the same packet of data, this way they take an average and it's more accurate. It is very complicated biology, something you wouldn't normally study until university.

EDIT: Take a look at this guide for a better explaination and this guide for installing and setting up the program (P.S. put team 50073 instead of the one that guide says)

**Josey Wales** · 04-13-2006, 12:04 PM

But how will the computer know? Or is it all simulated as if the computer was acting as a person, with living proteins?

**Chrono6456** · 04-13-2006, 12:05 PM

K, i joined the team

**Jammie** · 04-13-2006, 12:09 PM

Originally Posted by Dr. Butcher

But how will the computer know? Or is it all simulated as if the computer was acting as a person, with living proteins?

I'm not too sure, I just know that I'm helping people. Isn't that all that matters?

**Chrono6456** · 04-13-2006, 12:10 PM

Originally Posted by Jammie

I'm not too sure, I just know that I'm helping people. Isn't that all that matters?

Exactly what i was about to say...

**Jammie** · 04-13-2006, 12:13 PM

Originally Posted by SpartanIIMark6

Exactly what i was about to say...

You know what they say, great minds think alike.

**Chrono6456** · 04-13-2006, 12:16 PM

I just pressed Ctrl alt delete, and saw my comp is running at 100% cpu usage, dont see that everyday, no wonder when all combined, it becomes one of the biggest supercomputers in the world

**Jammie** · 04-13-2006, 12:20 PM

You can set it to only use your cpu when your PC is idle. If you right click on the icon --> Configure --> advanced. From there you can change the core priority. If you put it down to "lowest possible" it uses about 1-2% when you're on your PC and 100% when you're not on it.

**PopeOfDope** · 04-13-2006, 12:35 PM

OK I'll try explain this stuff to you guys.

A lot of stuff in our body is made out of proteins. Proteins are made up of a chain of molecules called amino acids. In total there are about 21 different amino acids. Proteins have 4 levels of structure.
1) The order of the amino acids
2) How the hydrogens on the amino acids interact
3) How other forces interact (disulphide bridges, Van Der Waals forces, weak ionic forces)
4) The number of chains and prosthetic groups.

These 4 factors influence the shape of the protein, if the shape of the protein is not right, it wont function properly.

Folding@home makes you arrange the 21 amino acids in a protein and then simulates how they fold according to the 4 principals I listed. As you can probably see, 21 amino acids and long protein chains means you have infinite combinations.
It is very useful to know this information as it can help a lot of people. Take a disease like Sickle Cell disease. This is when your Haemoglobin (the stuff that binds to oxygen in red blood cells) becomes messed up and makes your blood cells sickle shape. The protein is 146 amino acids long, the difference between normal haemoglobin and sickle hameoglobin is only 1 amino acid difference.

Once I get my AMD X2 4200+ I'll start folding, Folding@home would kill my PC right now

**cyanide** · 04-13-2006, 12:48 PM

yeah, ive joined too.
plus im putting it on the front page...

qj.net must be on the top of the contributors list :)

**cyanide** · 04-13-2006, 01:10 PM

cmon ba*tards, start contributing

**Jammie** · 04-13-2006, 01:18 PM

Your name wont appear on the team list until you complete a work unit, and it could be a while for me considering I've got a 10000 frame work unit.

**cyanide** · 04-13-2006, 01:35 PM

heh, ive got a 12500 frame work unit...
im getting one more pc soon...
will be kickass with 3 pcs working in tandem :)

**Jammie** · 04-13-2006, 01:46 PM

I got 2 systems running for the same username, that's how I got 29 work units so quickly.

**cyanide** · 04-13-2006, 02:13 PM

http://www.qj.net/QJ-NET-s-very-own-...g/49/aid/21635 :)

**Jammie** · 04-13-2006, 02:34 PM

Thanks for posting that on the front page. We're sure to get a few more people interested now. Also, I got my name on the front page :mrgreen: lol.

**cyanide** · 04-13-2006, 03:13 PM

well it still kinda sucks because it never made the top of the main qj.net blog...
the article was delayed, and thats why, the newer articles were on top...

**modcase** · 04-13-2006, 10:03 PM

I started running this program tonight, my pc's bound to rack up a number of hours for the cause. ;)

**Josey Wales** · 04-13-2006, 10:27 PM

Originally Posted by cyanide

heh, ive got a 12500 frame work unit...
im getting one more pc soon...
will be kickass with 3 pcs working in tandem :)

I have 50000 >.>

What do I win?

**Jammie** · 04-13-2006, 11:12 PM

a 50000frame WU means that each frame will take less time (about 20 seconds each), but in total the WU will take longer (50000*20=1000000 seconds to complete the WU).

**Josey Wales** · 04-13-2006, 11:22 PM

Im not sure what that means but, like you said, if its going to help people - whats the difference?

Ill get it hooked up to my others computers when I can

**marv101** · 04-14-2006, 01:26 PM

For those who don't understand proteins and their folding, listen up. I'm a biology and chemistry student so I know exactly what they're on about. I'll try to put it in laymens terms.

Basically, proteins are 3D structures consisting of one or more polypeptide chains, which in turn contain many amino acids linked together in a chain. To form the protein, the polypeptide chains twist and fold to form a unique shape. This shape is determined by what is attached to each individual amino acid (known as the Residual group, or R group). Different R groups will bond differently with one another, and it's these that give the protein their shape (intermolecular bonds, NOT intramolecular).

Mutations occur in the DNA, and the result of this is that there is a possibility of an amino acid being swapped with another, or a whole load of amino acids being completely different (especially if it's a deletion or addition mutation). Because of the different amino acid(s), there are different R groups. Different R groups result in a different shape.

So what's shape got to do with it? Unlike some other chemicals in the body, proteins mainly react (or rather cause a reaction) due to their shape. This is especially true for enzymes (which are just proteins, but have a specific function). Enzymes have something known as an 'active site'. This what causes the enzyme to break down other molecules by the molecule fitting into this site and undergoing a reaction which requires less energy than usual. With different R groups, the shape changes, and thus the active site changes. If the active site is changed too much, the molecules no longer fit inside. Thus the reactions do not take place. This is where diseases come into it. The body needs these products either to use them, or just be rid of the molecule in the first place. So if the body needs the reactants, something now isn't happening correctly, if it all. An example is Cystic Fibrosis which results in really thick mucus, so it's hard to breathe, and sufferers can suffocate. (It's caused by a change in the shape of a protein in the membrane of cells (specifically epithelial cells), so that Chloride ions can't move out of the cell. This means water moves into the cell (because of the high concentration of Cl- in the cell compared to out). This draws water from outside, specifically from the mucus, making it thick).

So as you can see, the way a protein folds is very important, and so this project is very important too. Errors in folding can lead to fatal diseases, so understanding how errors occur, whether it be due to the R group, or a different factor entired, is crucial. Please help.

Wanna know more detail, PM me

**Jammie** · 04-15-2006, 03:42 AM

Wow, that's complicated

. At least we don't have to know much about that to run F@H.

EDIT: We have our first WU completed, congrats to modcase

**gracz54** · 04-15-2006, 04:51 AM

zerg rush, ill contribute too ;) started running it

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