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    Modeling Protein Folding Pathways

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    Publication date
    2015-05-01
    Author
    Towse, Clare-Louise
    Daggett, V.
    Keyword
    Forced unfolding simulations; Molecular dynamics simulation; Protein folding; Protein simulation methodology
    Peer-Reviewed
    Yes
    
    Metadata
    Show full item record
    Abstract
    This chapter gives an introduction to protein simulation methodology aimed at experimentalists and graduate students new to in silico investigations. More emphasis is placed on the knowledge needed to select appropriate simulation protocols, leaving theoretical and mathematical depth for other texts to take care of. The chapter explains some of the more practical considerations of performing simulations of proteins, in particular, the additional considerations required when studying protein folding where nonnative environments are modeled. Forced unfolding simulations are highly relevant and invaluable in characterizing proteins naturally exposed to mechanical stress as a component of their biological function. The chapter illustrates this utility by discussing research that has been done primarily on the giant muscle protein titin. Using Molecular dynamics (MD) simulations to investigate protein folding faces two main challenges. The most obvious relates to the timescale of protein folding and the computational expense required for adequate sampling.
    URI
    http://hdl.handle.net/10454/11549
    Version
    No full-text in the repository
    Citation
    Towse C and Daggett V (2015) Modeling Protein Folding Pathways. In: Parrill AL and Lipkowitz KB (Eds.) Reviews in Computational Chemistry. Vol 28. Hoboken, NJ, US: John Wiley & Sons, Inc.
    Link to publisher’s version
    http://dx.doi.org/10.1002/9781118889886.ch3
    Type
    Book chapter
    Collections
    Life Sciences Publications

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