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post #1671 of 2102
Well my computer stopped earlier than i thought.. I need to reload the FAH it just stops and i haven't checked into why yet
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post #1672 of 2102
Lol...we won first place. Sheesh.

Everyone! We MUST loose October! Even if we have to work at it!
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post #1673 of 2102
Yeah, I couldn't believe we still took first place either! I'm pretty sure someone else will win this month, unless everyone stops folding.

So place your bets, who will the winner be for October?
post #1674 of 2102
Thread Starter 
lol now that we told everyone we weren't folding we should just to piss em off lmao! but seriously i think it'll be 'just because'
    
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post #1675 of 2102
The hilarious thing is my folding rig is running fine. No glitches. ***????!!
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post #1676 of 2102
I think i set somethin up wrong when i went to fah6 I'm only getting the 206 pointers now???
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post #1677 of 2102
Don't forget to use the -smp flag with the fah6 client. The 206 pointers are standard single core WUs.
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post #1678 of 2102
Quote:
Originally Posted by Taeric View Post
Don't forget to use the -smp flag with the fah6 client. The 206 pointers are standard single core WUs.
I wish you had a REP button Taeric you helped me so many times.. thanks thats what i was missing. i became too use to just the ./fah5 and ran it at ./fah6 without the -smp so now i'm back in business
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post #1679 of 2102
Ok, today marks the end of my electrical billing cycle. I'm going to start revving my engine. Load new Ubuntu client, do some test folding. Everyone ready to slap the other teams silly?
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post #1680 of 2102
Hello all!

Haven't been here for a quite a time. I've been taking a bioinformatics class and wanted to share with you what I have learned. This is just a tiny introductory portion. I'll post more of these as I see opportunity. It is really badly written, so please bear with my bad grammar.


I’ve been studying bioinformatics and protein structures over this semester. Here are some basics that might help you understand the folding mechanism better. The most basics ( I am sure most of you know what I will be talking about ) is the basic protein structure. Protein is made up of Amino Acids. There are 20 kinds of amino acids (there are variations but the others are rarely used and very specialized) in our body. There are four structures to a protein. The linear sequence is called the primary structure. The secondary structure has to deal with the hydrogen bonding. Bunch of amino acids can interact with each other in three unique way, alpha-helix, beta-sheet, loops. (hit the wikipedia for more information) Each amino acid has its special properties and this can be used to decipher which region of a protein may be helix, sheets, or neither. Once the secondary structure is solved, all other interactions of the molecule kicks in to solve the rest of the structure, such as disulfide bond between two cysteine residues. Quaternary structure is formed when multiple proteins interact with each other to form a bigger protein.

Now, on to the folding! Why is folding needed when there is human genome project? Human genome project is like a blueprint for a building, whereas the protein structure is the actual building. Also, DNA gives us different kind of information, which is mostly used to define differences between species or individuals but not as to how our body function. Protein structures must be solved to learn about what our body is doing. Just like we cannot tell how it would feel to live in a building from a blueprint, we do not know what DNA means. Building protein structure is tremendously difficult. Just to give a numerical example:

Let’s consider that each amino acid has one hinge that can turn (like a ball in a socket). Each hinge can be in any angle (which makes the possibility infinity), but I will simplify this and imagine there are 10 possible configuration of this hinge. Average Proteins may have 300 amino acid residues. The possible structure of this 300-amino acid primary sequence is 10^300. The number of people on the planet is in order of 10^9, and time elapsed in the universe in seconds is 10^18. Computer can compute 10^10 commands in a second. We’ll never find all possible conformation of this proteins.

But, let’s imagine human can magically solve all possible conformations of this protein. Another problem emerges: we don’t have a complete energy equation. Molecule wants to stay at its lowest energy state. This is why we don’t see rock jumping up and down, why we cannot walk through a wall, why cars can run on the road, and why global warming happens. If we had infinite number of possible protein conformation mapped out, we would have to score each prediction by calculating interaction between each molecule. If an amino acid had 5 atoms, 300-residue protein will have 1500 atoms. Number of interactions will be 1500! (factorial). We’ll never find all possible energy state of this protein.

But, lets imagine human can magically find all the energy states of this protein. Another problem emerges: this protein is in our body interacting with millions of other molecules. In our body, there are proteins called chaperones which help the proteins fold. We would have to know in which mechanism these chaperones help folding. Also, There are water molecules floating around, which makes the previous energy function incorrect. Again, we’ll never find the correct conformation.

Through all this obstacles of impossibility, Stanford (ssss, our nemesis) somehow wrote efficient algorithm to calculate the protein structure. This is F@H.

Currently, there are more than 4 millions genes coded and calculated (this I will explain in the future), yet we have about 40,000 protein structure. This discrepancy will only increase exponentially if we don’t find a efficient way to solve protein structures.

Bioinformatics deals with writing algorithms and programs that will approach this problem in a completely different way. (to be continued.. I must go to class now.)

Have a nice day!
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