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@ARTICLE{Fatafta:905717,
      author       = {Fatafta, Hebah and Samantray, Suman and Sayyed-Ahmad,
                      Abdallah and Coskuner-Weber, Orkid and Strodel, Birgit},
      title        = {{C}hapter {F}ive - {M}olecular simulations of {IDP}s:
                      {F}rom ensemble generation to {IDP} interactions leading to
                      disorder-to-order transitions},
      journal      = {Progress in molecular biology and translational science},
      volume       = {183},
      issn         = {1877-1173},
      address      = {Amsterdam ˜[u.a.]œ},
      publisher    = {Elsevier},
      reportid     = {FZJ-2022-00942},
      pages        = {135-185},
      year         = {2021},
      abstract     = {Intrinsically disordered proteins (IDPs) lack a
                      well-defined three-dimensional structure but do exhibit some
                      dynamical and structural ordering. The structural plasticity
                      of IDPs indicates that entropy-driven motions are crucial
                      for their function. Many IDPs undergo function-related
                      disorder-to-order transitions upon by their interaction with
                      specific binding partners. Approaches that are based on both
                      experimental and theoretical tools enable the biophysical
                      characterization of IDPs. Molecular simulations provide
                      insights into IDP structural ensembles and disorder-to-order
                      transition mechanisms. However, such studies depend strongly
                      on the chosen force field parameters and simulation
                      techniques. In this chapter, we provide an overview of IDP
                      characteristics, review all-atom force fields recently
                      developed for IDPs, and present molecular dynamics-based
                      simulation methods that allow IDP ensemble generation as
                      well as the characterization of disorder-to-order
                      transitions. In particular, we introduce metadynamics,
                      replica exchange molecular dynamics simulations, and also
                      kinetic models resulting from Markov State modeling, and
                      provide various examples for the successful application of
                      these simulation methods to IDPs.},
      cin          = {IBI-7},
      ddc          = {530},
      cid          = {I:(DE-Juel1)IBI-7-20200312},
      pnm          = {5244 - Information Processing in Neuronal Networks
                      (POF4-524)},
      pid          = {G:(DE-HGF)POF4-5244},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {34656328},
      UT           = {WOS:000748722300006},
      doi          = {10.1016/bs.pmbts.2021.06.003},
      url          = {https://juser.fz-juelich.de/record/905717},
}