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post #1681 of 2102
Quote:
Originally Posted by Chaogod87 View Post
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!

Isn't decoding the genome minor compared to decoding the protein blueprints?
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post #1682 of 2102
Quote:
Originally Posted by FrankenPC View Post
Isn't decoding the genome minor compared to decoding the protein blueprints?
Decoding Genome:
1) take a cell and isolate the DNA
2) blast the DNAs into pieces
3) take pieces of DNAs and overlap whichever region matches
---- ----------- -----------
---- -------- ----- ------ -------
----- ----- ---------------- ----
---------- ---------

4) then assume that this is the DNA of this cell


Decoding protein primary structure
1) take the DNA and find its promoter and termination site - DNA has these sites to allow polymerases to transcribe these DNA into mRNA (messenger)
2) these mRNA is identified before and after splicing.
Splicing - these mRNA is composed of introns and exons. introns are the garbage, they contain useless information and must be cut out before the RNA is translated into protein. These are assumed to have evolutionary purposes.
3) take the spliced mRNA and find out the protein primary structure
every 3 nucleotide (functional unit) in mRNA is called a codon. there are 4 kinds of nucleotides and 20 kinds of amino acids. Logically, you would need 3 nucleotides because 4*4*4 = 64 > 20. These codons then calls for the amino acid. The mechanism is unimportant at the moment.

The protein blueprint is rather easy to determine - not a lot of computing power or man-hour.




How are you doing, Franken?
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post #1683 of 2102
Doing crappy.


Hey gang, got my electrical bill. No change. Folding does nothing but add heat to my house.
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post #1684 of 2102
Thread Starter 
so you'll be back in Nov. right?
    
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post #1685 of 2102
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Originally Posted by cowboyzkickazz View Post
so you'll be back in Nov. right?
Yeah, there is no reason not to.
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post #1686 of 2102
We need to break the 250K barrier... you all realize that right?
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post #1687 of 2102
Thread Starter 
I'm going to sell my crucial that i bought recently and try to get 2 more gb of g.skill i like it better... I don't know if I'll be folding quite as much as i had been I'm plannign to start gaming a little more but I should still break 40k
    
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post #1688 of 2102
Ok, I'm folding again at the ~60K a month speed. Ready for next month. How is everyone else doing?
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post #1689 of 2102
I'm kinda in limbo at the moment, sold my E6600. Worse case, I can fold 4 console versions on my quad.

I'll keep you posted....
post #1690 of 2102
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Originally Posted by Compaddict View Post
I'm kinda in limbo at the moment, sold my E6600. Worse case, I can fold 4 console versions on my quad.

I'll keep you posted....
You can only fold 2 cores obviously.

So Cowboy is non-commital, you are in limbo. Is everyone getting tired of folding here? What's up soldiers? Getting tired of MARCHING UP AND DOWN THE SQUARE? Would you rather be at the movies eh? Out on a date?

Well, I'm not tired, I'm going to MARCH UP AND DOWN THE SQUARE!
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