protein folding
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@TheAzn5 Agreed! I'm sitting in it right now, and I'm riveted!
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DR. MALLERy"S CLASS IS THE BEST!
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However, two atoms that are separated far away do not interact effectively, so to save time, usually, only two atoms close enough to each other will be calculated. (That's called short range interation, and long range interaction would be ignored or estimated roughly) Still, you have a huge number of atom pairs to calculate.
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To simulate any process at atomic level, we need to calculate the interaction between each pair of atoms in the model system. Think about how many atom pair do you have if there are 100000 atoms in your system?!
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Because there are too many atoms in the system we simulate: protein, water molecules...
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Try an analogue computer.
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If you can't even understand why that statement is wrong, how are you even aware of proteins?
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at what FrameRate does this video animates? 75Hz?
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@mangamagne this is exactly what knowledge based approaches use. They break up the sequence into fragments and see how these fragments usually fold. They then stochastically reassemble the fragments into a protein that meets the criteria of the energy function in question. Rosetta@home does this exact thing.
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Folding@Home ftw!
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Because of the huge amount of variables. If you change the position of 1 atom, you have to recalculated the forces acting within the entire protein molecule.
So to find the structure in which is a protein is completely stable (ie all forces are in an equilibrium) , you have to recalculated an enormous amount of times. At least, that's how I understood it ;)
Twabi2 3 years ago 8
why does it take 2 weeks with a super computer to simulate 1 microsecond of protein folding?
Westonci 3 years ago 8