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PDB_REDO :
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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 ...
Numbers
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LIBRIS-ID:oai:DiVA.org:uu-129054
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-129054URI
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https://doi.org/10.1107/S0021889809008784DOI
Supplementary language notes
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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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 ...)
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Salzemann, Jean
(author)
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Bloch, Vincent
(author)
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Stockinger, Heinz
(author)
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Berglund, Ann-CharlottUppmax, SLV, Uppsala Universitet
(author)
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Blanchet, Christophe
(author)
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Bongcam-Rudloff, ErikUppsala universitet,Institutionen för cell- och molekylärbiologi
(author)
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Combet, Christophe
(author)
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Da Costa, L
(author)
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Deleage, Gilbert
(author)
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Diarena, Matteo
(author)
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Fabbretti, Roberto
(author)
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Fettahi, Geraldine
(author)
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Flegel, Volker
(author)
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Gisel, Andreas
(author)
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Kasam, Vinod
(author)
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Kervinen, Timo
(author)
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Korpelainen, Eija
(author)
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Mattila, Kimmo
(author)
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Pagni, Marco
(author)
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Reichstadt, Matthieu
(author)
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Breton, Vincent
(author)
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Tickle, J
(author)
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Vriend, Gert
(author)
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Uppmax, SLV, Uppsala UniversitetInstitutionen för cell- och molekylärbiologi
(creator_code:org_t)
Related titles
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In:Journal of applied crystallography42, s. 376-3840021-88981600-5767
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Joosten, Robbie ...
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Salzemann, Jean
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Bloch, Vincent
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Stockinger, Hein ...
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Berglund, Ann-Ch ...
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Blanchet, Christ ...
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Bongcam-Rudloff, ...
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Combet, Christop ...
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Da Costa, L
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Deleage, Gilbert
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Diarena, Matteo
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Fabbretti, Rober ...
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Fettahi, Geraldi ...
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Flegel, Volker
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Gisel, Andreas
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Kasam, Vinod
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Kervinen, Timo
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Korpelainen, Eij ...
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Mattila, Kimmo
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Pagni, Marco
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Reichstadt, Matt ...
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Breton, Vincent
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Tickle, J
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Vriend, Gert
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Uppsala University