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Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations

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Molecular Modeling of Proteins

Part of the book series: Methods Molecular Biology™ ((MIMB,volume 443))

Summary

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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Acknowledgments

This work was supported by research grants from the National Institutes of Health (NIH; GM64458 and GM67168 to YD).

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  1. Genome Center, University of California, Davis, CA

    Hongxing Lei & Yong Duan

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  1. Hongxing Lei
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  2. Yong Duan
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Andreas Kukol

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Lei, H., Duan, Y. (2008). Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations. In: Kukol, A. (eds) Molecular Modeling of Proteins. Methods Molecular Biology™, vol 443. Humana Press. https://doi.org/10.1007/978-1-59745-177-2_15

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  • DOI: https://doi.org/10.1007/978-1-59745-177-2_15

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-864-5

  • Online ISBN: 978-1-59745-177-2

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