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@ARTICLE{vanderWeg:1005449,
      author       = {van der Weg, Karel J and Gohlke, Holger},
      title        = {{T}op{E}nzyme: a framework and database for structural
                      coverage of the functional enzyme space},
      journal      = {Bioinformatics},
      volume       = {39},
      number       = {3},
      issn         = {0266-7061},
      address      = {Oxford},
      publisher    = {Oxford Univ. Press},
      reportid     = {FZJ-2023-01480},
      pages        = {btad116},
      year         = {2023},
      abstract     = {MotivationTopEnzyme is a database of structural enzyme
                      models created with TopModel and is linked to the
                      SWISS-MODEL repository and AlphaFold Protein Structure
                      Database to provide an overview of structural coverage of
                      the functional enzyme space for over 200,000 enzyme models.
                      It allows the user to quickly obtain representative
                      structural models for $60\%$ of all known enzyme
                      functions.ResultsWe assessed the models with TopScore and
                      contributed 9039 good-quality and 1297 high-quality
                      structures. Furthermore, we compared these models to
                      AlphaFold2 models with TopScore and found that the TopScore
                      differs only by 0.04 on average in favor of AlphaFold2. We
                      tested TopModel and AlphaFold2 for targets not seen in the
                      respective training databases and found that both methods
                      create qualitatively similar structures. When no
                      experimental structures are available, this database will
                      facilitate quick access to structural models across the
                      currently most extensive structural coverage of the
                      functional enzyme space within Swiss-Prot.},
      cin          = {JSC / IBG-4 / NIC},
      ddc          = {570},
      cid          = {I:(DE-Juel1)JSC-20090406 / I:(DE-Juel1)IBG-4-20200403 /
                      I:(DE-Juel1)NIC-20090406},
      pnm          = {5111 - Domain-Specific Simulation $\&$ Data Life Cycle Labs
                      (SDLs) and Research Groups (POF4-511) / 2171 - Biological
                      and environmental resources for sustainable use (POF4-217) /
                      Forschergruppe Gohlke $(hkf7_20200501)$},
      pid          = {G:(DE-HGF)POF4-5111 / G:(DE-HGF)POF4-2171 /
                      $G:(DE-Juel1)hkf7_20200501$},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {36883717},
      UT           = {WOS:000954379300002},
      doi          = {10.1093/bioinformatics/btad116},
      url          = {https://juser.fz-juelich.de/record/1005449},
}