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Could somebody with more expertise explain how modern day protein folding simulations work? (Like Rosetta) I'm only familiar with the folding@home method of bru
by Lramseyer 10y ago
Could somebody with more expertise explain how modern day protein folding simulations work? (Like Rosetta) I'm only familiar with the folding@home method of brute force molecular dynamics simulation. What kind of computational power does it take to go from an RNA sequence or polypeptide chain to stable protein with these algorithms?
This has always been a subject that has fascinated me, ever since high school when my biology teacher told us about folding@home. I went into computer hardware, so I always saw this problem as a computational power problem. I always believed that if we could figure this out, we could do a lot of cool things like make nanotubes and cure diseases. I saw it as the key to the nanotechnology revolution.
- zgcarvalho 10y agoRosetta is a software for protein structure prediction, not for protein folding simulation. There are a lot of hipothesis about protein folding, but the mechanism is unknown yet. So simulations using molecular dynamics can help us to understand how proteins fold. On the other hand, protein structure prediction methods like Rosetta try to create high quality atomic models of proteins without follow a physical model. The goal is a good final model, not the fold event. Rosetta uses a method of fragment assembly where fragments (few amino acids) of proteins with structure solved experimentally (usually X-ray crystalography) are assembled to create the new structure. The fragments have sequences of residues (amino acids) identicals or similar to the protein being modelled. This is an optimization process and uses methods like Simulated annealing. So, computational power is very important to explore a lot of protein conformations.