review · Methods in molecular biology · 2012

Enhanced Sampling Algorithms

Cited by 67Abstract and details only

Abstract

In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. Enhanced conformational sampling techniques are thus in great demand. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review uses of the generalized-ensemble algorithms in biomolecular systems. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present various extensions of these three generalized-ensemble algorithms. The effectiveness of the methods is tested with short peptide and protein systems.

Cite this paper

APA 7

Mitsutake, A., Mori, Y., & Okamoto, Y. (2012). Enhanced Sampling Algorithms. Methods in molecular biology, 924, 153–195. https://doi.org/10.1007/978-1-62703-017-5_7

MLA 9

Mitsutake, Ayori, et al. “Enhanced Sampling Algorithms.” Methods in molecular biology, vol. 924, 2012, pp. 153–95, https://doi.org/10.1007/978-1-62703-017-5_7.

Chicago

Mitsutake, Ayori, Y. Mori, and Yuko Okamoto. 2012. “Enhanced Sampling Algorithms.” Methods in molecular biology 924: 153–95. https://doi.org/10.1007/978-1-62703-017-5_7.

Harvard

Mitsutake, A., Mori, Y. and Okamoto, Y. (2012) ‘Enhanced Sampling Algorithms’, Methods in molecular biology, 924, pp. 153–195. Available at: https://doi.org/10.1007/978-1-62703-017-5_7.

BibTeX

@article{mitsutake2012enhanced,
  title = {{Enhanced Sampling Algorithms}},
  author = {Mitsutake, Ayori and Mori, Y. and Okamoto, Yuko},
  journal = {Methods in molecular biology},
  volume = {924},
  pages = {153--195},
  year = {2012},
  doi = {10.1007/978-1-62703-017-5_7}
}

Made from the index record. Check names, capitalisation and page numbers against the paper. Need another style? AI for Research has over 10,000.