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@ARTICLE{Schepers:877528,
      author       = {Schepers, Bastian and Gohlke, Holger},
      title        = {{AMBER}-{DYES} in {AMBER}: {I}mplementation of fluorophore
                      and linker parameters into {A}mber{T}ools},
      journal      = {The journal of chemical physics},
      volume       = {152},
      number       = {22},
      issn         = {0021-9606},
      address      = {Woodbury, NY},
      publisher    = {American Institute of Physics},
      reportid     = {FZJ-2020-02264},
      pages        = {221103},
      year         = {2020},
      abstract     = {Molecular dynamics (MD) simulations of explicit
                      representations of fluorescent dyes attached via a linker to
                      a protein allow, e.g., probing commonly used approximations
                      for dye localization and/or orientation or modeling Förster
                      resonance energy transfer. However, setting up and
                      performing such MD simulations with the AMBER suite of
                      biomolecular simulation programs has remained challenging
                      due to the unavailability of an easy-to-use set of
                      parameters within AMBER. Here, we adapted the AMBER-DYES
                      parameter set derived by Graen et al. [J. Chem. Theory
                      Comput. 10, 5505 (2014)] into “AMBER-DYES in AMBER” to
                      generate a force field applicable within AMBER for commonly
                      used fluorescent dyes and linkers attached to a protein. In
                      particular, the computationally efficient graphics
                      processing unit (GPU) implementation of the AMBER MD engine
                      can now be exploited to overcome sampling issues of dye
                      movements. The implementation is compatible with
                      state-of-the-art force fields such as GAFF, GAFF2, ff99SB,
                      ff14SB, lipid17, and $GLYCAM_06j,$ which allows simulating
                      post-translationally modified proteins and/or
                      protein–ligand complexes and/or proteins in membrane
                      environments. It is applicable with frequently used water
                      models such as TIP3P, TIP4P, TIP4P-Ew, and OPC. For ease of
                      use, a LEaP-based workflow was created, which allows
                      attaching (multiple) dye/linker combinations to a protein
                      prior to further system preparation steps. Following the
                      parameter development described by Graen et al. [J. Chem.
                      Theory Comput. 10, 5505 (2014)] and the adaptation steps
                      described here, AMBER-DYES in AMBER can be extended by
                      additional linkers and fluorescent molecules.},
      cin          = {NIC / JSC / IBI-7},
      ddc          = {540},
      cid          = {I:(DE-Juel1)NIC-20090406 / I:(DE-Juel1)JSC-20090406 /
                      I:(DE-Juel1)IBI-7-20200312},
      pnm          = {511 - Computational Science and Mathematical Methods
                      (POF3-511) / Forschergruppe Gohlke $(hkf7_20170501)$ / DFG
                      project 267205415 - SFB 1208: Identität und Dynamik von
                      Membransystemen - von Molekülen bis zu zellulären
                      Funktionen},
      pid          = {G:(DE-HGF)POF3-511 / $G:(DE-Juel1)hkf7_20170501$ /
                      G:(GEPRIS)267205415},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:32534525},
      UT           = {WOS:000541908200002},
      doi          = {10.1063/5.0007630},
      url          = {https://juser.fz-juelich.de/record/877528},
}