Hydrophobic aided replica exchange: An efficient algorithm for protein folding in explicit solvent

The hydrophobic aided replica exchange method (HAREM) is introduced to accelerate the simulation of all-atom protein folding in explicit solvent. The method is applied to a small representative protein, the alpha-helix 3K(I), and it is found that the HAREM method successfully folds the protein with 4 ns, while the regular replicas exchange method does not fold the same protein within 5 ns, even with many more replicas.