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@ARTICLE{Lugmayr:486213,
      author       = {Lugmayr, Wolfgang and Kotov, Vadim and Goessweiner-Mohr,
                      Nikolaus and Wald, Jiri and DiMaio, Frank and Marlovits,
                      Thomas},
      title        = {{S}tar{M}ap: a user-friendly workflow for {R}osetta-driven
                      molecular structure refinement},
      journal      = {Nature protocols},
      volume       = {18},
      number       = {1},
      issn         = {1754-2189},
      address      = {Basingstoke},
      publisher    = {Nature Publishing Group},
      reportid     = {PUBDB-2022-07155},
      pages        = {239 - 264},
      year         = {2023},
      note         = {Waiting for fulltext},
      abstract     = {Cryogenic electron microscopy (cryo-EM) data represent
                      density maps of macromolecular systems at atomic or
                      near-atomic resolution. However, building and refining 3D
                      atomic models by using data from cryo-EM maps is not
                      straightforward and requires significant hands-on experience
                      and manual intervention. We recently developed StarMap, an
                      easy-to-use interface between the popular structural display
                      program ChimeraX and Rosetta, a powerful molecular modeling
                      engine. StarMap offers a general approach for refining
                      structural models of biological macromolecules into cryo-EM
                      density maps by combining Monte Carlo sampling with local
                      density-guided optimization, Rosetta-based all-atom
                      refinement and real-space B-factor calculations in a
                      straightforward workflow. StarMap includes options for
                      structural symmetry, local refinements and independent model
                      validation. The overall quality of the refinement and the
                      structure resolution is then assessed via analytical
                      outputs, such as magnification calibration (pixel size
                      calibration) and Fourier shell correlations. Z-scores
                      reported by StarMap provide an easily interpretable
                      indicator of the goodness of fit for each residue and can be
                      plotted to evaluate structural models and improve local
                      residue refinements, as well as to identify flexible regions
                      and potentially functional sites in large macromolecular
                      complexes. The protocol requires general computer skills,
                      without the need for coding expertise, because most parts of
                      the workflow can be operated by clicking tabs within the
                      ChimeraX graphical user interface. Time requirements for the
                      model refinement depend on the size and quality of the input
                      data; however, this step can typically be completed within 1
                      d. The analytical parts of the workflow are completed within
                      minutes.},
      cin          = {FS-CS / CSSB-UKE-TM},
      ddc          = {610},
      cid          = {I:(DE-H253)FS-CS-20210408 /
                      I:(DE-H253)CSSB-UKE-TM-20210520},
      pnm          = {633 - Life Sciences – Building Blocks of Life: Structure
                      and Function (POF4-633)},
      pid          = {G:(DE-HGF)POF4-633},
      experiment   = {EXP:(DE-MLZ)NOSPEC-20140101},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:36323866},
      UT           = {WOS:000878062700001},
      doi          = {10.1038/s41596-022-00757-9},
      url          = {https://bib-pubdb1.desy.de/record/486213},
}