using Folding@Home rn, but I don’t quite understand how that works.
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I remember that program.
I ran it on my ps3 for ages.
The idea is that it runs calculations on how the compounds they are trying to create can react and runs the same simulation 100s of times to rule out radicals etc.
Or so I was lead to believe.
Okay so basically, your DNA encodes all the information for keeping you alive. It does this by storing the information necessary to make proteins. Proteins are little molecular machines do do everything that’s required to be alive, the most well known proteins are probably enzymes. Proteins are made as a long chain of amino acids, 21 in total, and the order they are put together is encoded in the DNA. Once the long chain of amino acids is formed, it needs to be arranged so that it takes the proper 3-D form, because it is the three dimensional arrangement in space that allows proteins to do their job. We call this process of taking the chain and making a specific shape “folding”.
Okay, so why is it important? As already explained, it is the protein’S 3-D shape that dictates how it works, often time the active amino acids on a protein are tend or hundreds of links (called residues) apart, but once they are folded they can be right next to each other. The problem is, the DNA sequence only tells us the order, not the 3-D arrangement. So we need to solve the “protein folding problem” to better predict what a protein will look like from only the associated DNA sequence (and that’s what you’re doing when you’re playing Fold It! or other similar games)!
Proteins are what the “blueprints” that are in our DNA are blueprints for. They are molecules that perform the vast majority of functions in our cells and consist of long strings of smaller parts known as amino acids. When proteins are created in our cells, they are created by linking these amino acids together one by one, and as this is happening, that long chain of amino acids begins folding into a specific shape that is crucial to the function of that protein.
We have sequenced the human genome, along with the genomes of hundreds of other species of life, and identified the genes in those genomes, so we know the amino acid sequences of most proteins. But because the physical shape of the protein is an important in its function, just knowing the sequences of these proteins doesn’t tell us everything we need to know about what they do and how they do it. The Folding@Home program is doing simulations to figure this out. Essentially, it starts with the protein sequence and then runs a physical simulation to try to reproduce the physics and chemistry that are occurring when that protein folds to predict what shape it will fold into. This is a very computationally intensive process, so the work is distributed across as many computers as possible.
Imagine a protein as a very long chain covered with hundreds of magnets of different sizes. All those magnets are pushing and pulling on each other, so rather than staying one long chain, the chain quickly clumps up. The shape of that clump is hugely important to the protein’s function, much like how a key has to be just the right shape to open a door. The weird thing is, because all those magnets interact, if you add or subtract or swap even one magnet, the shape of the whole protein can change dramatically.
In reality, they’re not just push vs pull magnets, but different amino acids that all interact differently with each other. As a result, having the list of amino acids in order that make up a protein (AKA a gene) doesn’t tell you what the protein will look like, because figuring out how huge numbers of amino acids will all interact with each other is very complicated, and it’s taken us a long time with the most advanced forms of computing to be able to do it.
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