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

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 present...

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Bibliographic Details
Published in:Journal of applied crystallography 2009-06, Vol.42 (3), p.376-384
Main Authors: Joosten, Robbie P., Salzemann, Jean, Bloch, Vincent, Stockinger, Heinz, Berglund, Ann-Charlott, Blanchet, Christophe, Bongcam-Rudloff, Erik, Combet, Christophe, Da Costa, Ana L., Deleage, Gilbert, Diarena, Matteo, Fabbretti, Roberto, Fettahi, Géraldine, Flegel, Volker, Gisel, Andreas, Kasam, Vinod, Kervinen, Timo, Korpelainen, Eija, Mattila, Kimmo, Pagni, Marco, Reichstadt, Matthieu, Breton, Vincent, Tickle, Ian J., Vriend, Gert
Format: Article
Language:English
Subjects:
Bioinformatics
Biologi
Biology
Computer Science
Crystal structure
Crystallography
Diffraction
grid computing
Life Sciences
Molecular biology
NATURAL SCIENCES
NATURVETENSKAP
Protein Data Bank
Proteins
Quantitative Methods
refinement
Research Papers
structure validation
X-ray crystallography
X-rays
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Summary: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.
ISSN:1600-5767
0021-8898
1600-5767
DOI:10.1107/S0021889809008784