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@ARTICLE{LaSala:841292,
      author       = {La Sala, Giuseppina and Decherchi, Sergio and De Vivo,
                      Marco and Rocchia, Walter},
      title        = {{A}llosteric {C}ommunication {N}etworks in {P}roteins
                      {R}evealed through {P}ocket {C}rosstalk {A}nalysis},
      journal      = {ACS central science},
      volume       = {3},
      number       = {9},
      issn         = {2374-7951},
      address      = {Washington, DC},
      publisher    = {ACS Publ.},
      reportid     = {FZJ-2017-08383},
      pages        = {949 - 960},
      year         = {2017},
      abstract     = {The detection and characterization of binding pockets and
                      allosteric communication in proteins is crucial for studying
                      biological regulation and performing drug design. Nowadays,
                      ever-longer molecular dynamics (MD) simulations are
                      routinely used to investigate the spatiotemporal evolution
                      of proteins. Yet, there is no computational tool that can
                      automatically detect all the pockets and potential
                      allosteric communication networks along these extended MD
                      simulations. Here, we use a novel and fully automated
                      algorithm that examines pocket formation, dynamics, and
                      allosteric communication embedded in microsecond-long MD
                      simulations of three pharmaceutically relevant proteins,
                      namely, PNP, A2A, and Abl kinase. This dynamic analysis uses
                      pocket crosstalk, defined as the temporal exchange of atoms
                      between adjacent pockets, along the MD trajectories as a
                      fingerprint of hidden allosteric communication networks.
                      Importantly, this study indicates that dynamic pocket
                      crosstalk analysis provides new mechanistic understandings
                      on allosteric communication networks, enriching the
                      available experimental data. Thus, our results suggest the
                      prospective use of this unprecedented dynamic analysis to
                      characterize transient binding pockets for structure-based
                      drug design},
      cin          = {IAS-5 / INM-9},
      ddc          = {540},
      cid          = {I:(DE-Juel1)IAS-5-20120330 / I:(DE-Juel1)INM-9-20140121},
      pnm          = {574 - Theory, modelling and simulation (POF3-574)},
      pid          = {G:(DE-HGF)POF3-574},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:28979936},
      UT           = {WOS:000411712800009},
      doi          = {10.1021/acscentsci.7b00211},
      url          = {https://juser.fz-juelich.de/record/841292},
}