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@ARTICLE{Do:201311,
      author       = {Do, Trang N. and Carloni, Paolo and Varani, Gabriele and
                      Bussi, Giovanni},
      title        = {{RNA}/{P}eptide {B}inding {D}riven by
                      {E}lectrostatics—{I}nsight from {B}idirectional {P}ulling
                      {S}imulations},
      journal      = {Journal of chemical theory and computation},
      volume       = {9},
      number       = {3},
      issn         = {1549-9626},
      address      = {Washington, DC},
      publisher    = {American Chemical Society (ACS)},
      reportid     = {FZJ-2015-03616},
      pages        = {1720 - 1730},
      year         = {2013},
      abstract     = {RNA/protein interactions play crucial roles in controlling
                      gene expression. They are becoming important targets for
                      pharmaceutical applications. Due to RNA flexibility and to
                      the strength of electrostatic interactions, standard docking
                      methods are insufficient. We here present a computational
                      method which allows studying the binding of RNA molecules
                      and charged peptides with atomistic, explicit-solvent
                      molecular dynamics. In our method, a suitable estimate of
                      the electrostatic interaction is used as an order parameter
                      (collective variable) which is then accelerated using
                      bidirectional pulling simulations. Since the electrostatic
                      interaction is only used to enhance the sampling, the
                      approximations used to compute it do not affect the final
                      accuracy. The method is employed to characterize the binding
                      of TAR RNA from HIV-1 and a small cyclic peptide. Our
                      simulation protocol allows blindly predicting the binding
                      pocket and pose as well as the binding affinity. The method
                      is general and could be applied to study other
                      electrostatics-driven binding events.},
      cin          = {GRS / IAS-5},
      ddc          = {540},
      cid          = {I:(DE-Juel1)GRS-20100316 / I:(DE-Juel1)IAS-5-20120330},
      pnm          = {899 - ohne Topic (POF2-899)},
      pid          = {G:(DE-HGF)POF2-899},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000316168700042},
      doi          = {10.1021/ct3009914},
      url          = {https://juser.fz-juelich.de/record/201311},
}