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    Transmembrane Helix Assembly by Window Exchange Umbrella Sampling

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    Issue Date
    2012-03-08
    Author
    Park, Soohyung
    Kim, Taehoon
    Im, Wonpil
    Publisher
    American Physical Society
    Type
    Article
    Article Version
    Scholarly/refereed, publisher version
    Published Version
    http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.108.108102
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    Abstract
    A method of window exchange umbrella sampling molecular dynamics simulation is employed for transmembrane helix assembly. An analytical expression for the average acceptance probability between neighboring windows is derived and combined with the first passage time optimization method to predetermine a parameter set in an optimal range. With the parameter set, the method provides a substantially more efficient sampling of helix-helix interfaces together with the potential of mean force along the helix-helix distance of a transmembrane helix-dimer model, compared to the umbrella sampling method.
    URI
    http://hdl.handle.net/1808/22462
    DOI
    https://doi.org/10.1103/PhysRevLett.108.108102
    Collections
    • Center for Computational Biology Scholarly Works [27]
    Citation
    Park, Soohyung, Taehoon Kim, and Wonpil Im. "Transmembrane Helix Assembly by Window Exchange Umbrella Sampling." Physical Review Letters 108.10 (2012): n. pag.

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    Contact KU ScholarWorks
    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    Image Credits
     

     

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