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PDB_REDO :
PDB_REDO : automated re-refinement of X-ray structure models in the PDB
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Joosten, Robbie P. (author)
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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-Charlott (author)
- Uppmax, SLV, Uppsala Universitet
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Blanchet, Christophe (author)
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- Bongcam-Rudloff, Erik (author)
- Uppsala universitet,Institutionen för cell- och molekylärbiologi
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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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(creator_code:org_t)
- 2009
- 2009
- English.
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In: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 42, s. 376-384
- Related links:
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
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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
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
Keyword
- Biology
- Biologi
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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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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show more...
-
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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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
- Articles in the publication
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Journal of appli ...
- By the university
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Uppsala University