Transmembrane Helix Assembly by Window Exchange Umbrella Sampling
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Issue Date
2012-03-08Author
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.108.108102Metadata
Show full item recordAbstract
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.
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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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