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@ARTICLE{DeVivo:820516,
      author       = {De Vivo, Marco and Masetti, Matteo and Bottegoni, Giovanni
                      and Cavalli, Andrea},
      title        = {{R}ole of {M}olecular {D}ynamics and {R}elated {M}ethods in
                      {D}rug {D}iscovery},
      journal      = {Journal of medicinal chemistry},
      volume       = {59},
      number       = {9},
      issn         = {1520-4804},
      address      = {Washington, DC},
      publisher    = {ACS},
      reportid     = {FZJ-2016-05808},
      pages        = {4035 - 4061},
      year         = {2016},
      abstract     = {Molecular dynamics (MD) and related methods are close to
                      becoming routine computational tools for drug discovery.
                      Their main advantage is in explicitly treating structural
                      flexibility and entropic effects. This allows a more
                      accurate estimate of the thermodynamics and kinetics
                      associated with drug–target recognition and binding, as
                      better algorithms and hardware architectures increase their
                      use. Here, we review the theoretical background of MD and
                      enhanced sampling methods, focusing on free-energy
                      perturbation, metadynamics, steered MD, and other methods
                      most consistently used to study drug–target binding. We
                      discuss unbiased MD simulations that nowadays allow the
                      observation of unsupervised ligand–target binding,
                      assessing how these approaches help optimizing target
                      affinity and drug residence time toward improved drug
                      efficacy. Further issues discussed include allosteric
                      modulation and the role of water molecules in ligand binding
                      and optimization. We conclude by calling for more
                      prospective studies to attest to these methods’ utility in
                      discovering novel drug candidates.},
      cin          = {IAS-5 / INM-9},
      ddc          = {540},
      cid          = {I:(DE-Juel1)IAS-5-20120330 / I:(DE-Juel1)INM-9-20140121},
      pnm          = {899 - ohne Topic (POF3-899)},
      pid          = {G:(DE-HGF)POF3-899},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000375969200002},
      pubmed       = {pmid:26807648},
      doi          = {10.1021/acs.jmedchem.5b01684},
      url          = {https://juser.fz-juelich.de/record/820516},
}