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@INPROCEEDINGS{deBruyn:903372,
      author       = {de Bruyn, Emile and Zimmermann, Olav and Grohe, Martin and
                      Rossetti, Giulia},
      title        = {{M}odelling {I}on-{R}esidue {I}nteraction in {I}mplicit
                      {S}olvation for {I}ntrinsically {D}isordered {P}roteins},
      school       = {RWTH Aachen},
      reportid     = {FZJ-2021-05061},
      year         = {2021},
      abstract     = {This project aims to develop a new implicit solvent model
                      that enables rapid and accurate exploration of the
                      conformational space of Intrinsically Disordered Proteins
                      (IDPs).IDPs are characterised by their structural
                      heterogeneity and visit diverse and transient conformational
                      ensembles. These proteins have attracted broad interest due
                      to their ubiquitous involvement in biological function and
                      dysfunction, including promising therapeutic targets. This
                      makes characterisation of IDPs' structure-function
                      relationships both essential and challenging.Molecular
                      Dynamics (MD) simulations are commonly used to explore the
                      conformational landscape of IDPs. These explorations mostly
                      overlook interactions between ions and solvent with
                      individual amino acid residues that reshape the energy
                      landscape and drive ensemble switching in IDPs. MD
                      simulations are also unfortunately slow to stabilise complex
                      aggregates of solvent and solutes, even though these
                      simulations are drastically reduced in complexity compared
                      to biological conditions. Ion motions have been identified
                      as a rate-determining step in the already large free energy
                      surface sample required, and as such impede the exploration
                      and study of IDP dynamics. Approaches to avoid this rate
                      determining step exist: coarse-grained models combined with
                      Monte Carlo (MC) simulation approaches have already proven
                      valuable in characterising several IDPs. Achieving finer
                      accuracy through atomistic MC simulations require implicit
                      or continuum solvent, which at present insufficiently model
                      the interactions between ions and residues, and therefore
                      cannot accurately explore IDPs’ conformational
                      landscape.To accurately model the effect of ions on
                      individual amino acid residues, this project uses existing
                      trajectory data and data from highly time-resolved
                      state-of-the-art MD simulations. The positional data within
                      MD trajectories are used as input for Machine Learning to
                      obtain data-driven parameters for a new implicit solvent
                      model.},
      month         = {Oct},
      date          = {2021-10-05},
      organization  = {INM $\&$ IBI Retreat 2021, Jülich
                       (Germany), 5 Oct 2021 - 6 Oct 2021},
      subtyp        = {After Call},
      cin          = {JSC / IAS-5 / INM-9},
      cid          = {I:(DE-Juel1)JSC-20090406 / I:(DE-Juel1)IAS-5-20120330 /
                      I:(DE-Juel1)INM-9-20140121},
      pnm          = {5112 - Cross-Domain Algorithms, Tools, Methods Labs (ATMLs)
                      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)POF4-5112 / G:(DE-Juel1)HDS-LEE-20190612},
      typ          = {PUB:(DE-HGF)24},
      url          = {https://juser.fz-juelich.de/record/903372},
}