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@ARTICLE{Wang:111912,
      author       = {Wang, Z. and Schröder, G.F.},
      title        = {{R}eal-space {R}efinement with {D}ire{X}: {F}rom {G}lobal
                      {F}itting to {S}ide-chain {I}mprovements},
      journal      = {Biopolymers},
      volume       = {97},
      issn         = {0006-3525},
      address      = {New York, NY},
      publisher    = {Wiley},
      reportid     = {PreJuSER-111912},
      pages        = {S687 - S697},
      year         = {2012},
      note         = {Record converted from VDB: 16.11.2012},
      abstract     = {Single-particle cryo-electron microscopy (cryo-EM) has
                      become an important tool to determine the structure of large
                      biomolecules and assemblies thereof. However, the achievable
                      resolution varies considerably over a wide range of about
                      3.5-20 Å. The interpretation of these intermediate- to
                      low-resolution density maps in terms of atomic models is a
                      big challenge and an area of active research. Here, we
                      present our real-space structure refinement program DireX,
                      which was developed primarily for cryo-EM-derived density
                      maps. The basic principle and its main features are
                      described. DireX employs Deformable Elastic Network (DEN)
                      restraints to reduce overfitting by decreasing the effective
                      number of degrees of freedom used in the refinement. Missing
                      or reduced density due to flexible parts of the protein can
                      lead to artifacts in the structure refinement, which is
                      addressed through the concept of restrained grouped
                      occupancy refinement. Furthermore, we describe the
                      performance of DireX in the 2010 Cryo-EM Modeling Challenge,
                      where we chose six density maps of four different proteins
                      provided by the Modeling Challenge exemplifying typical
                      refinement results at a large resolution range from 3 to 23
                      Å.},
      keywords     = {Antigens, Viral: chemistry / Aquaporins: chemistry / Capsid
                      Proteins: chemistry / Chaperonin 10: chemistry / Chaperonin
                      60: chemistry / Cryoelectron Microscopy: methods / Eye
                      Proteins: chemistry / Models, Molecular / Proteins:
                      chemistry / Software / Antigens, Viral (NLM Chemicals) /
                      Aquaporins (NLM Chemicals) / Capsid Proteins (NLM Chemicals)
                      / Chaperonin 10 (NLM Chemicals) / Chaperonin 60 (NLM
                      Chemicals) / Eye Proteins (NLM Chemicals) / Proteins (NLM
                      Chemicals) / VP6 protein, Rotavirus (NLM Chemicals) /
                      aquaporin 0 (NLM Chemicals) / J (WoSType)},
      cin          = {ICS-6},
      ddc          = {570},
      cid          = {I:(DE-Juel1)ICS-6-20110106},
      pnm          = {Funktion und Dysfunktion des Nervensystems / BioSoft:
                      Makromolekulare Systeme und biologische
                      Informationsverarbeitung},
      pid          = {G:(DE-Juel1)FUEK409 / G:(DE-Juel1)FUEK505},
      shelfmark    = {Biochemistry $\&$ Molecular Biology / Biophysics},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:22696405},
      UT           = {WOS:000305183000005},
      doi          = {10.1002/bip.22046},
      url          = {https://juser.fz-juelich.de/record/111912},
}