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@ARTICLE{Sengupta:858917,
      author       = {Sengupta, Ushnish and Strodel, Birgit},
      title        = {{M}arkov models for the elucidation of allosteric
                      regulation},
      journal      = {Philosophical transactions of the Royal Society of London /
                      B Biological sciences Series B},
      volume       = {373},
      number       = {1749},
      issn         = {1471-2970},
      address      = {London},
      reportid     = {FZJ-2018-07753},
      pages        = {20170178 -},
      year         = {2018},
      abstract     = {Allosteric regulation refers to the process where the
                      effect of binding of a ligand at one site of a protein is
                      transmitted to another, often distant, functional site. In
                      recent years, it has been demonstrated that allosteric
                      mechanisms can be understood by the conformational ensembles
                      of a protein. Molecular dynamics (MD) simulations are often
                      used for the study of protein allostery as they provide an
                      atomistic view of the dynamics of a protein. However, given
                      the wealth of detailed information hidden in MD data, one
                      has to apply a method that allows extraction of the
                      conformational ensembles underlying allosteric regulation
                      from these data. Markov state models are one of the most
                      promising methods for this purpose. We provide a short
                      introduction to the theory of Markov state models and review
                      their application to various examples of protein allostery
                      studied by MD simulations. We also include a discussion of
                      studies where Markov modelling has been employed to analyse
                      experimental data on allosteric regulation. We conclude our
                      review by advertising the wider application of Markov state
                      models to elucidate allosteric mechanisms, especially since
                      in recent years it has become straightforward to construct
                      such models thanks to software programs like PyEMMA and
                      MSMBuilder.This article is part of a discussion meeting
                      issue 'Allostery and molecular machines'.},
      cin          = {ICS-6},
      ddc          = {570},
      cid          = {I:(DE-Juel1)ICS-6-20110106},
      pnm          = {551 - Functional Macromolecules and Complexes (POF3-551)},
      pid          = {G:(DE-HGF)POF3-551},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:29735732},
      UT           = {WOS:000431688500006},
      doi          = {10.1098/rstb.2017.0178},
      url          = {https://juser.fz-juelich.de/record/858917},
}