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  • Joosten, Robbie P. (author)

PDB_REDO : automated re-refinement of X-ray structure models in the PDB

  • Article/chapterEnglish2009

Publisher, publication year, extent ...

  • 2009
  • printrdacarrier

Numbers

  • LIBRIS-ID:oai:DiVA.org:uu-129054
  • https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-129054URI
  • https://doi.org/10.1107/S0021889809008784DOI

Supplementary language notes

  • Language:English
  • Summary in:English

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  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Salzemann, Jean (author)
  • Bloch, Vincent (author)
  • Stockinger, Heinz (author)
  • Berglund, Ann-CharlottUppmax, SLV, Uppsala Universitet (author)
  • Blanchet, Christophe (author)
  • Bongcam-Rudloff, ErikUppsala universitet,Institutionen för cell- och molekylärbiologi (author)
  • Combet, Christophe (author)
  • Da Costa, L (author)
  • Deleage, Gilbert (author)
  • Diarena, Matteo (author)
  • Fabbretti, Roberto (author)
  • Fettahi, Geraldine (author)
  • Flegel, Volker (author)
  • Gisel, Andreas (author)
  • Kasam, Vinod (author)
  • Kervinen, Timo (author)
  • Korpelainen, Eija (author)
  • Mattila, Kimmo (author)
  • Pagni, Marco (author)
  • Reichstadt, Matthieu (author)
  • Breton, Vincent (author)
  • Tickle, J (author)
  • Vriend, Gert (author)
  • Uppmax, SLV, Uppsala UniversitetInstitutionen för cell- och molekylärbiologi (creator_code:org_t)

Related titles

  • In:Journal of applied crystallography42, s. 376-3840021-88981600-5767

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