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@ARTICLE{Hoffmann:134962,
      author       = {Hoffmann, Falk and Strodel, Birgit},
      title        = {{P}rotein structure prediction using global optimization by
                      basin-hopping with {NMR} shift restraints},
      journal      = {The journal of chemical physics},
      volume       = {138},
      number       = {025102},
      issn         = {0021-9606},
      address      = {Melville, NY},
      publisher    = {American Institute of Physics},
      reportid     = {FZJ-2013-02977},
      pages        = {1-7},
      year         = {2013},
      abstract     = {Computational methods that utilize chemical shifts to
                      produce protein structures at atomic resolution have
                      recently been introduced. In the current work, we exploit
                      chemical shifts by combining the basin-hopping approach to
                      global optimization with chemical shift restraints using a
                      penalty function. For three peptides, we demonstrate that
                      this approach allows us to find near-native structures from
                      fully extended structures within 10 000 basin-hopping
                      steps. The effect of adding chemical shift restraints is
                      that the α and β secondary structure elements form within
                      1000 basin-hopping steps, after which the orientation of the
                      secondary structure elements, which produces the tertiary
                      contacts, is driven by the underlying protein force field.
                      We further show that our chemical shift-restraint BH
                      approach also works for incomplete chemical shift
                      assignments, where the information from only one chemical
                      shift type is considered. For the proper implementation of
                      chemical shift restraints in the basin-hopping approach, we
                      determined the optimal weight of the chemical shift penalty
                      energy with respect to the CHARMM force field in conjunction
                      with the FACTS solvation model employed in this study. In
                      order to speed up the local energy minimization procedure,
                      we developed a function, which continuously decreases the
                      width of the chemical shift penalty function as the
                      minimization progresses. We conclude that the basin-hopping
                      approach with chemical shift restraints is a promising
                      method for protein structure prediction.},
      cin          = {ICS-6},
      ddc          = {540},
      cid          = {I:(DE-Juel1)ICS-6-20110106},
      pnm          = {452 - Structural Biology (POF2-452)},
      pid          = {G:(DE-HGF)POF2-452},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000313642500071},
      doi          = {10.1063/1.4773406},
      url          = {https://juser.fz-juelich.de/record/134962},
}