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@ARTICLE{Kutzner:810120,
      author       = {Kutzner, Carsten and Köpfer, David A. and Machtens,
                      Jan-Philipp and de Groot, Bert L. and Song, Chen and
                      Zachariae, Ulrich},
      title        = {{I}nsights into the function of ion channels by
                      computational electrophysiology simulations},
      journal      = {Biochimica et biophysica acta / Biomembranes},
      volume       = {1858},
      number       = {7 B},
      issn         = {0005-2736},
      address      = {Amsterdam},
      publisher    = {Elsevier},
      reportid     = {FZJ-2016-02995},
      pages        = {1741 - 1752},
      year         = {2016},
      abstract     = {Ion channels are of universal importance for all cell types
                      and play key roles in cellular physiology and pathology.
                      Increased insight into their functional mechanisms is
                      crucial to enable drug design on this important class of
                      membrane proteins, and to enhance our understanding of some
                      of the fundamental features of cells. This review presents
                      the concepts behind the recently developed simulation
                      protocol Computational Electrophysiology (CompEL), which
                      facilitates the atomistic simulation of ion channels in
                      action. In addition, the review provides guidelines for its
                      application in conjunction with the molecular dynamics
                      software package GROMACS. We first lay out the rationale for
                      designing CompEL as a method that models the driving force
                      for ion permeation through channels the way it is
                      established in cells, i.e., by electrochemical ion gradients
                      across the membrane. This is followed by an outline of its
                      implementation and a description of key settings and
                      parameters helpful to users wishing to set up and conduct
                      such simulations. In recent years, key mechanistic and
                      biophysical insights have been obtained by employing the
                      CompEL protocol to address a wide range of questions on ion
                      channels and permeation. We summarize these recent findings
                      on membrane proteins, which span a spectrum from highly
                      ion-selective, narrow channels to wide diffusion pores.
                      Finally we discuss the future potential of CompEL in light
                      of its limitations and strengths. This article is part of a
                      Special Issue entitled: Membrane Proteins edited by J.C.
                      Gumbart and Sergei Noskov.},
      cin          = {ICS-4},
      ddc          = {570},
      cid          = {I:(DE-Juel1)ICS-4-20110106},
      pnm          = {551 - Functional Macromolecules and Complexes (POF3-551)},
      pid          = {G:(DE-HGF)POF3-551},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000377233200017},
      pubmed       = {pmid:26874204},
      doi          = {10.1016/j.bbamem.2016.02.006},
      url          = {https://juser.fz-juelich.de/record/810120},
}