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@ARTICLE{Hoang:1039818,
      author       = {Hoang, Gia Linh and Röck, Manuel and Tancredi, Aldo and
                      Magauer, Thomas and Mandelli, Davide and Schulz, Jörg B.
                      and Krauss, Sybille and Rossetti, Giulia and Tollinger,
                      Martin and Carloni, Paolo},
      title        = {{R}efining {L}igand {P}oses in {RNA}/{L}igand {C}omplexes
                      of {P}harmaceutical {R}elevance: {A} {P}erspective by
                      {QM}/{MM} {S}imulations and {NMR} {M}easurements},
      journal      = {The journal of physical chemistry letters},
      volume       = {16},
      number       = {7},
      issn         = {1948-7185},
      address      = {Washington, DC},
      publisher    = {ACS},
      reportid     = {FZJ-2025-01815},
      pages        = {1702 - 1708},
      year         = {2025},
      abstract     = {Predicting the binding poses of ligands targeting RNAs is
                      challenging. Here, we propose that using first-principles
                      quantum mechanics/molecular mechanics (QM/MM) simulations,
                      which incorporate automatically polarization effects, can
                      help refine the structural determinants of ligand/RNA
                      complexes in aqueous solution. In fact, recent advances in
                      massively parallel computer architectures (such as exascale
                      machines), combined with the power of machine learning, are
                      greatly expanding the domain of applicability of these types
                      of notoriously expensive simulations. We corroborate this
                      proposal by carrying out a QM/MM-based study on a ligand
                      targeting CAG repeat-RNA, involved in Huntington’s
                      disease. The calculations indeed show a clear improvement in
                      the ligand binding properties, and they are consistent with
                      the NMR measurements, also performed here. Thus, this type
                      of approach may be useful for practical applications in the
                      design of ligands targeting RNA in the near future.},
      cin          = {INM-11 / INM-9},
      ddc          = {530},
      cid          = {I:(DE-Juel1)INM-11-20170113 / I:(DE-Juel1)INM-9-20140121},
      pnm          = {5241 - Molecular Information Processing in Cellular Systems
                      (POF4-524) / DFG project G:(GEPRIS)491111487 -
                      Open-Access-Publikationskosten / 2025 - 2027 /
                      Forschungszentrum Jülich (OAPKFZJ) (491111487)},
      pid          = {G:(DE-HGF)POF4-5241 / G:(GEPRIS)491111487},
      typ          = {PUB:(DE-HGF)16},
      doi          = {10.1021/acs.jpclett.4c03456},
      url          = {https://juser.fz-juelich.de/record/1039818},
}