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@ARTICLE{deBruyn:1006780,
      author       = {de Bruyn, Emile and Dorn, Anton and Zimmermann, Olav and
                      Rossetti, Giulia},
      title        = {{SPEADI}: {A}ccelerated {A}nalysis of {IDP}-{I}on
                      {I}nteractions from {MD}-{T}rajectories},
      journal      = {Biology},
      volume       = {12},
      number       = {4},
      issn         = {2079-7737},
      address      = {Basel},
      publisher    = {MDPI},
      reportid     = {FZJ-2023-01833},
      pages        = {581 -},
      year         = {2023},
      abstract     = {The disordered nature of Intrinsically Disordered Proteins
                      (IDPs) makes their structural ensembles particularly
                      susceptible to changes in chemical environmental conditions,
                      often leading to an alteration of their normal functions. A
                      Radial Distribution Function (RDF) is considered a standard
                      method for characterizing the chemical environment
                      surrounding particles during atomistic simulations, commonly
                      averaged over an entire or part of a trajectory. Given their
                      high structural variability, such averaged information might
                      not be reliable for IDPs. We introduce the Time-Resolved
                      Radial Distribution Function (TRRDF), implemented in our
                      open-source Python package SPEADI, which is able to
                      characterize dynamic environments around IDPs. We use SPEADI
                      to characterize the dynamic distribution of ions around the
                      IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular
                      Dynamics (MD) simulations, and some of their selected
                      mutants, showing that local ion–residue interactions play
                      an important role in the structures and behaviors of IDPs.},
      cin          = {JSC / IAS-5 / INM-9},
      ddc          = {570},
      cid          = {I:(DE-Juel1)JSC-20090406 / I:(DE-Juel1)IAS-5-20120330 /
                      I:(DE-Juel1)INM-9-20140121},
      pnm          = {5111 - Domain-Specific Simulation $\&$ Data Life Cycle Labs
                      (SDLs) and Research Groups (POF4-511) / HDS LEE - Helmholtz
                      School for Data Science in Life, Earth and Energy (HDS LEE)
                      (HDS-LEE-20190612)},
      pid          = {G:(DE-HGF)POF4-5111 / G:(DE-Juel1)HDS-LEE-20190612},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {37106781},
      UT           = {WOS:000978909400001},
      doi          = {10.3390/biology12040581},
      url          = {https://juser.fz-juelich.de/record/1006780},
}