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@ARTICLE{Bertalan:943339,
      author       = {Bertalan, Éva and Lesca, Elena and Schertler, Gebhard F.
                      X. and Bondar, Ana-Nicoleta},
      title        = {{C}-{G}raphs {T}ool with {G}raphical {U}ser {I}nterface to
                      {D}issect {C}onserved {H}ydrogen-{B}ond {N}etworks:
                      {A}pplications to {V}isual {R}hodopsins},
      journal      = {Journal of chemical information and modeling},
      volume       = {61},
      number       = {11},
      issn         = {0095-2338},
      address      = {Washington, DC},
      publisher    = {American Chemical Society},
      reportid     = {FZJ-2023-00945},
      pages        = {5692 - 5707},
      year         = {2021},
      abstract     = {Dynamic hydrogen-bond networks provide proteins with
                      structural plasticity required to translate signals such as
                      ligand binding into a cellular response or to transport ions
                      and larger solutes across membranes and, thus, are of
                      central interest to understand protein reaction mechanisms.
                      Here, we present C-Graphs, an efficient tool with graphical
                      user interface that analyzes data sets of static protein
                      structures or of independent numerical simulations to
                      identify conserved, vs unique, hydrogen bonds and
                      hydrogen-bond networks. For static structures, which may
                      belong to the same protein or to proteins with different
                      sequences, C-Graphs uses a clustering algorithm to identify
                      sites of the hydrogen-bond network where waters are
                      conserved among the structures. Using C-Graphs, we identify
                      an internal protein–water hydrogen-bond network common to
                      static structures of visual rhodopsins and adenosine A2A G
                      protein-coupled receptors (GPCRs). Molecular dynamics
                      simulations of a visual rhodopsin indicate that the
                      conserved hydrogen-bond network from static structure can
                      recruit dynamic hydrogen bonds and extend throughout most of
                      the receptor. We release with this work the code for
                      C-Graphs and its graphical user interface.},
      cin          = {IAS-5 / INM-9},
      ddc          = {540},
      cid          = {I:(DE-Juel1)IAS-5-20120330 / I:(DE-Juel1)INM-9-20140121},
      pnm          = {5241 - Molecular Information Processing in Cellular Systems
                      (POF4-524)},
      pid          = {G:(DE-HGF)POF4-5241},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {34670076},
      UT           = {WOS:000757001900035},
      doi          = {10.1021/acs.jcim.1c00827},
      url          = {https://juser.fz-juelich.de/record/943339},
}