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@ARTICLE{Korshunova:891480,
      author       = {Korshunova, Ksenia and Carloni, Paolo},
      title        = {{L}igand {A}ffinities within the {O}pen-{B}oundary
                      {M}olecular {M}echanics/{C}oarse-{G}rained {F}ramework
                      ({I}): {A}lchemical {T}ransformations within the
                      {H}amiltonian {A}daptive {R}esolution {S}cheme},
      journal      = {The journal of physical chemistry / B},
      volume       = {125},
      number       = {3},
      issn         = {1520-5207},
      address      = {Washington, DC},
      publisher    = {Soc.},
      reportid     = {FZJ-2021-01554},
      pages        = {789 - 797},
      year         = {2021},
      abstract     = {Our recently developed Open-Boundary Molecular
                      Mechanics/Coarse Grained (OB-MM/CG) framework predicts
                      ligand poses in important pharmaceutical targets, such as
                      G-protein Coupled Receptors, even when experimental
                      structural information is lacking. The approach, which is
                      based on GROMOS and AMBER force fields, allows for
                      grand-canonical simulations of protein–ligand complexes by
                      using the Hamiltonian Adaptive Resolution Scheme (H-AdResS)
                      for the solvent. Here, we present a key step toward the
                      estimation of ligand binding affinities for their targets
                      within this approach. This is the implementation of the
                      H-AdResS in the GROMACS code. The accuracy of our
                      implementation is established by calculating hydration free
                      energies of several molecules in water by means of
                      alchemical transformations. The deviations of the GROMOS-
                      and AMBER-based H-AdResS results from the reference fully
                      atomistic simulations are smaller than the accuracy of the
                      force field and/or they are in the range of the published
                      results. Importantly, our predictions are in good agreement
                      with experimental data. The current implementation paves the
                      way to the use of the OB-MM/CG framework for the study of
                      large biological systems.},
      cin          = {IAS-5 / INM-9},
      ddc          = {530},
      cid          = {I:(DE-Juel1)IAS-5-20120330 / I:(DE-Juel1)INM-9-20140121},
      pnm          = {524 - Molecular and Cellular Information Processing
                      (POF4-524)},
      pid          = {G:(DE-HGF)POF4-524},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {33443434},
      UT           = {WOS:000614308000010},
      doi          = {10.1021/acs.jpcb.0c09805},
      url          = {https://juser.fz-juelich.de/record/891480},
}