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Protein-Folding Dynamics: Overview of Molecular Simulation Techniques

2006; Annual Reviews; Volume: 58; Issue: 1 Linguagem: Inglês

10.1146/annurev.physchem.58.032806.104614

1545-1593

Harold A. Scheraga, Mey Khalili, Adam Liwo,

RNA and protein synthesis mechanisms

Molecular dynamics (MD) is an invaluable tool with which to study protein folding in silico. Although just a few years ago the dynamic behavior of a protein molecule could be simulated only in the neighborhood of the experimental conformation (or protein unfolding could be simulated at high temperature), the advent of distributed computing, new techniques such as replica-exchange MD, new approaches (based on, e.g., the stochastic difference equation), and physics-based reduced models of proteins now make it possible to study protein-folding pathways from completely unfolded structures. In this review, we present algorithms for MD and their extensions and applications to protein-folding studies, using all-atom models with explicit and implicit solvent as well as reduced models of polypeptide chains.