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@ARTICLE{Strodel:9867,
      author       = {Strodel, B. and Bauer, M.S. and Fejer, S.N. and Koslover,
                      E.F. and Wales, D.J.},
      title        = {{I}nterpolation {S}chemes for {P}eptide {R}earrangements},
      journal      = {The journal of chemical physics},
      volume       = {132},
      issn         = {0021-9606},
      address      = {Melville, NY},
      publisher    = {American Institute of Physics},
      reportid     = {PreJuSER-9867},
      pages        = {054101},
      year         = {2010},
      note         = {M.B. gratefully acknowledges the Gates Cambridge Trust for
                      financial support.},
      abstract     = {A variety of methods (in total seven) comprising different
                      combinations of internal and Cartesian coordinates are
                      tested for interpolation and alignment in connection
                      attempts for polypeptide rearrangements. We consider
                      Cartesian coordinates, the internal coordinates used in
                      CHARMM, and natural internal coordinates, each of which has
                      been interfaced to the OPTIM code and compared with the
                      corresponding results for united-atom force fields. We show
                      that aligning the methylene hydrogens to preserve the sign
                      of a local dihedral angle, rather than minimizing a distance
                      metric, provides significant improvements with respect to
                      connection times and failures. We also demonstrate the
                      superiority of natural coordinate methods in conjunction
                      with internal alignment. Checking the potential energy of
                      the interpolated structures can act as a criterion for the
                      choice of the interpolation coordinate system, which reduces
                      failures and connection times significantly.},
      keywords     = {Algorithms / Artificial Intelligence / Computer Simulation
                      / Image Enhancement / Image Interpretation,
                      Computer-Assisted / Mathematics: methods / Molecular
                      Sequence Data / Pattern Recognition, Automated / Peptides:
                      chemistry / Protein Conformation / Protein Folding /
                      Thermodynamics / Peptides (NLM Chemicals) / J (WoSType)},
      cin          = {ISB-3},
      ddc          = {540},
      cid          = {I:(DE-Juel1)VDB942},
      pnm          = {Funktion und Dysfunktion des Nervensystems / BioSoft:
                      Makromolekulare Systeme und biologische
                      Informationsverarbeitung},
      pid          = {G:(DE-Juel1)FUEK409 / G:(DE-Juel1)FUEK505},
      shelfmark    = {Physics, Atomic, Molecular $\&$ Chemical},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:20136299},
      UT           = {WOS:000274319900002},
      doi          = {10.1063/1.3273617},
      url          = {https://juser.fz-juelich.de/record/9867},
}