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@ARTICLE{Marchetto:890217,
      author       = {Marchetto, Alessandro and Si Chaib, Zeineb and Rossi, Carlo
                      Alberto and Ribeiro, Rui and Pantano, Sergio and Rossetti,
                      Giulia and Giorgetti, Alejandro},
      title        = {{CGMD} {P}latform: {I}ntegrated {W}eb {S}ervers for the
                      {P}reparation, {R}unning, and {A}nalysis of
                      {C}oarse-{G}rained {M}olecular {D}ynamics {S}imulations},
      journal      = {Molecules},
      volume       = {25},
      number       = {24},
      issn         = {1420-3049},
      address      = {Basel},
      publisher    = {MDPI70206},
      reportid     = {FZJ-2021-00806},
      pages        = {5934 -},
      year         = {2020},
      abstract     = {Advances in coarse-grained molecular dynamics (CGMD)
                      simulations have extended the use of computational studies
                      on biological macromolecules and their complexes, as well as
                      the interactions of membrane protein and lipid complexes at
                      a reduced level of representation, allowing longer and
                      larger molecular dynamics simulations. Here, we present a
                      computational platform dedicated to the preparation,
                      running, and analysis of CGMD simulations. The platform is
                      built on a completely revisited version of our Martini
                      coarsE gRained MembrAne proteIn Dynamics (MERMAID) web
                      server, and it integrates this with other three dedicated
                      services. In its current version, the platform expands the
                      existing implementation of the Martini force field for
                      membrane proteins to also allow the simulation of soluble
                      proteins using the Martini and the SIRAH force fields.
                      Moreover, it offers an automated protocol for carrying out
                      the backmapping of the coarse-grained description of the
                      system into an atomistic one.},
      cin          = {IAS-5 / JSC / INM-9},
      ddc          = {540},
      cid          = {I:(DE-Juel1)IAS-5-20120330 / I:(DE-Juel1)JSC-20090406 /
                      I:(DE-Juel1)INM-9-20140121},
      pnm          = {574 - Theory, modelling and simulation (POF3-574) / 511 -
                      Computational Science and Mathematical Methods (POF3-511)},
      pid          = {G:(DE-HGF)POF3-574 / G:(DE-HGF)POF3-511},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {33333836},
      UT           = {WOS:000603266000001},
      doi          = {10.3390/molecules25245934},
      url          = {https://juser.fz-juelich.de/record/890217},
}