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@ARTICLE{Mohanty:133447,
      author       = {Mohanty, Sandipan and Meinke, Jan and Zimmermann, Olav},
      title        = {{F}olding of {T}op7 in unbiased all-atom {M}onte {C}arlo
                      simulations},
      journal      = {Proteins},
      volume       = {81},
      number       = {8},
      issn         = {0887-3585},
      address      = {New York, NY},
      publisher    = {Wiley-Liss},
      reportid     = {FZJ-2013-01895},
      pages        = {1446 - 1456},
      year         = {2013},
      abstract     = {For computational studies of protein folding, proteins with
                      both helical and β-sheet secondary structure elements are
                      very challenging, since they expose subtle biases of the
                      physical models. Here we present reproducible folding of a
                      92 residue α/β protein (residues 3–94 of Top7, PDB ID:
                      1QYS) in computer simulations starting from random initial
                      conformations using a transferable physical model which has
                      been previously shown to describe the folding and
                      thermodynamic properties of about 20 other smaller proteins
                      of different folds. Top7 is a de novo designed protein with
                      two α-helices and a 5 stranded β-sheet. Experimentally it
                      is known to be unusually stable for its size, and its
                      folding transition distinctly deviates from the two state
                      behaviour commonly seen in natural single domain proteins.
                      In our all-atom implicit solvent parallel tempering Monte
                      Carlo simulations, Top7 shows a rapid transition to a group
                      of states with high native-like secondary structure, and a
                      much slower subsequent transition to the native state with a
                      root mean square deviation of about 3.5 Å from the
                      experimentally determined structure. Consistent with
                      experiments, we find Top7 to be thermally extremely stable,
                      although the simulations also find a large number of very
                      stable non-native states with high native-like secondary
                      structure.},
      cin          = {JSC},
      ddc          = {540},
      cid          = {I:(DE-Juel1)JSC-20090406},
      pnm          = {411 - Computational Science and Mathematical Methods
                      (POF2-411)},
      pid          = {G:(DE-HGF)POF2-411},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000329220400014},
      pubmed       = {pmid:23553942},
      doi          = {10.1002/prot.24295},
      url          = {https://juser.fz-juelich.de/record/133447},
}