Rosetta is a software for protein structure prediction, not for protein folding simulation. There are a lot of hipothesis about protein folding, but the mechani

Rosetta 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.