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@ARTICLE{Petrovi:858914,
      author       = {Petrović, Dušan and Wang, Xue and Strodel, Birgit},
      title        = {{H}ow accurately do force fields represent protein side
                      chain ensembles?},
      journal      = {Proteins},
      volume       = {86},
      number       = {9},
      issn         = {0887-3585},
      address      = {New York, NY},
      publisher    = {Wiley-Liss},
      reportid     = {FZJ-2018-07750},
      pages        = {935 - 944},
      year         = {2018},
      abstract     = {Although the protein backbone is the most fundamental part
                      of the structure, the fine-tuning of side-chain
                      conformations is important for protein function, for
                      example, in protein-protein and protein-ligand interactions,
                      and also in enzyme catalysis. While several benchmarks
                      testing the performance of protein force fields for side
                      chain properties have already been published, they often
                      considered only a few force fields and were not tested
                      against the same experimental observables; hence, they are
                      not directly comparable. In this work, we explore the
                      ability of twelve force fields, which are different flavors
                      of AMBER, CHARMM, OPLS, or GROMOS, to reproduce average
                      rotamer angles and rotamer populations obtained from
                      extensive NMR studies of the 3 J and residual dipolar
                      coupling constants for two small proteins: ubiquitin and
                      GB3. Based on a total of 196 μs sampling time, our
                      results reveal that all force fields identify the correct
                      side chain angles, while the AMBER and CHARMM force fields
                      clearly outperform the OPLS and GROMOS force fields in
                      estimating rotamer populations. The three best force fields
                      for representing the protein side chain dynamics are AMBER
                      14SB, AMBER 99SB*-ILDN, and CHARMM36. Furthermore, we
                      observe that the side chain ensembles of buried amino acid
                      residues are generally more accurately represented than
                      those of the surface exposed residues.},
      cin          = {ICS-6 / JARA-HPC},
      ddc          = {570},
      cid          = {I:(DE-Juel1)ICS-6-20110106 / $I:(DE-82)080012_20140620$},
      pnm          = {551 - Functional Macromolecules and Complexes (POF3-551) /
                      Computational Enzyme Design $(jics69_20151101)$},
      pid          = {G:(DE-HGF)POF3-551 / $G:(DE-Juel1)jics69_20151101$},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:29790608},
      UT           = {WOS:000446996700004},
      doi          = {10.1002/prot.25525},
      url          = {https://juser.fz-juelich.de/record/858914},
}