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  • Title: Protein folding and unfolding by all-atom molecular dynamics simulations.
    Author: Lei H, Duan Y.
    Journal: Methods Mol Biol; 2008; 443():277-95. PubMed ID: 18446293.
    Abstract:
    Computational protein folding can be classified into pathway and sampling approaches. Here, we use the AMBER simulation package as an example to illustrate the protocols for all-atom molecular simulations of protein folding, including system setup, simulation, and analysis. We introduced two traditional pathway approaches: ab inito folding and high-temperature unfolding. The popular replica exchange method was chosen to represent sampling approaches. Our emphasis is placed on the analysis of the simulation trajectories, and some in-depth discussions are provided for commonly encountered problems.
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