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@MISC{deBruyn:1034039,
      author       = {de Bruyn, Emile and Dorn, Anton and Rossetti, Giulia and
                      Fernandez, Claudio Oscar and Outeiro, Tiago Fleming and
                      Schulz, Jörg B. and Carloni, Paolo},
      title        = {{M}olecular {D}ynamics {T}rajectories {E}xploring the
                      {I}mpact of {P}hosphorylation on the {P}hysiological {F}orm
                      of {H}uman alpha-{S}ynuclein in {A}queous {S}olution},
      address      = {Jülich},
      publisher    = {Forschungszentrum Jülich},
      reportid     = {FZJ-2024-06869},
      year         = {2024},
      note         = {Published under the Creative Commons Attribution 4.0
                      International license.},
      abstract     = {Primary data for the publication 'Impact of Phosphorylation
                      on the Physiological Form of Human alpha-Synuclein in
                      Aqueous Solution' by de Bruyn, Dorn, Rossetti, Fernandez,
                      Outeiro, Schulz and Carloni. Submitted to the Journal of
                      Chemical Information and Modeling. Included are all GROMACS
                      input files, parameterised topologies, starting and final
                      configurations, and trajectories for the lowest temperature
                      replica (at 300 K, lowest of 32 replicas between 300-500 K
                      exchanging according to the REST2 algorithm (Wang et al.
                      2011)). The data is split into three archives:
                      $all_atom_trajectories.zip$ contains all input files and all
                      atom trajectories including solvent trajectories written at
                      100 ps intervals $protein+ion_trajectories.zip$ contains
                      configuration/non-parameterised topologies and trajectories
                      excluding solvent, but including ions trajectories written
                      at 10 ps intervals $additional_simulations.zip$ contains the
                      all atom trajectories and input files, and solvent-free
                      trajectories above, for the additional simulations in the
                      Supplemental Information of the article: includes the
                      DES-Amber-based simulations with 64 replicas between 300-600
                      K, and a99SB-disp-based simulations   Folders are named
                      according to the following top level scheme: DES-Amber
                      simulations/ Simulations created using the DES-Amber force
                      field (Tucker et al. 2022) a99SB-disp
                      simulations/ SImulations created using the a99SB-disp force
                      field for Intrinsically Disordered Proteins (IDPs)
                      (Robustelli et al. 2018) Sub-folders follow the following
                      scheme: AS/ Simulations of the physiological form
                      of wild-type Human α-Synuclein unphosphorylated
                      pAS/ Simulations of the physiological form of
                      wild-type Human α-Synuclein phosphorylated at S129 with
                      double negative charge pASH/ Simulations of the
                      physiological form of wild-type Human α-Synuclein
                      (a99SB-disp simulations only) phosphorylated at S129 with a
                      single negative charge (monoprotonated)},
      keywords     = {Structural biology (Other) / Biophysics (Other) / PTM
                      (Other) / Phosphorylated Proteins (Other) / Phosphorylation
                      (Other) / aSyn (Other) / AS (Other) / Alpha-Synuclein
                      (Other) / Molecular Dynamics (Other)},
      cin          = {JSC / INM-9 / INM-11},
      cid          = {I:(DE-Juel1)JSC-20090406 / I:(DE-Juel1)INM-9-20140121 /
                      I:(DE-Juel1)INM-11-20170113},
      pnm          = {5111 - Domain-Specific Simulation $\&$ Data Life Cycle Labs
                      (SDLs) and Research Groups (POF4-511) / 5112 - Cross-Domain
                      Algorithms, Tools, Methods Labs (ATMLs) and Research Groups
                      (POF4-511) / DFG project G:(GEPRIS)390729940 - EXC 2067:
                      Multiscale Bioimaging: Von molekularen Maschinen zu
                      Netzwerken erregbarer Zellen (390729940) / HDS LEE -
                      Helmholtz School for Data Science in Life, Earth and Energy
                      (HDS LEE) (HDS-LEE-20190612) / SFB 1286 B08 - Definition von
                      Kaskaden molekularer Veränderungen bei Synucleinopathien
                      während der Neurodegeneration (B08) (386961151)},
      pid          = {G:(DE-HGF)POF4-5111 / G:(DE-HGF)POF4-5112 /
                      G:(GEPRIS)390729940 / G:(DE-Juel1)HDS-LEE-20190612 /
                      G:(GEPRIS)386961151},
      typ          = {PUB:(DE-HGF)32},
      doi          = {10.5281/zenodo.12605635},
      url          = {https://juser.fz-juelich.de/record/1034039},
}