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@ARTICLE{Voronin:888464,
      author       = {Voronin, Arthur and Weiel, Marie and Schug, Alexander},
      title        = {{I}ncluding residual contact information into
                      replica-exchange {MD} simulations significantly enriches
                      native-like conformations},
      journal      = {PLOS ONE},
      volume       = {15},
      number       = {11},
      issn         = {1932-6203},
      address      = {San Francisco, California, US},
      publisher    = {PLOS},
      reportid     = {FZJ-2020-04932},
      pages        = {e0242072 -},
      year         = {2020},
      abstract     = {Proteins are complex biomolecules which perform critical
                      tasks in living organisms. Knowledge of a protein’s
                      structure is essential for understanding its physiological
                      function in detail. Despite the incredible progress in
                      experimental techniques, protein structure determination is
                      still expensive, time-consuming, and arduous. That is why
                      computer simulations are often used to complement or
                      interpret experimental data. Here, we explore how in silico
                      protein structure determination based on replica-exchange
                      molecular dynamics (REMD) can benefit from including contact
                      information derived from theoretical and experimental
                      sources, such as direct coupling analysis or NMR
                      spectroscopy. To reflect the influence from erroneous and
                      noisy data we probe how false-positive contacts influence
                      the simulated ensemble. Specifically, we integrate varying
                      numbers of randomly selected native and non-native contacts
                      and explore how such a bias can guide simulations towards
                      the native state. We investigate the number of contacts
                      needed for a significant enrichment of native-like
                      conformations and show the capabilities and limitations of
                      this method. Adhering to a threshold of approximately $75\%$
                      true-positive contacts within a simulation, we obtain an
                      ensemble with native-like conformations of high quality. We
                      find that contact-guided REMD is capable of delivering
                      physically reasonable models of a protein’s structure.},
      cin          = {JSC},
      ddc          = {610},
      cid          = {I:(DE-Juel1)JSC-20090406},
      pnm          = {511 - Computational Science and Mathematical Methods
                      (POF3-511) / Forschergruppe Schug $(hkf6_20200501)$},
      pid          = {G:(DE-HGF)POF3-511 / $G:(DE-Juel1)hkf6_20200501$},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {33196676},
      UT           = {WOS:000595266800006},
      doi          = {10.1371/journal.pone.0242072},
      url          = {https://juser.fz-juelich.de/record/888464},
}