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Research article - Peer-reviewed, 2009

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

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, Geraldine; Flegel, Volker; Gisel, Andreas; Kasam, Vinod; Kervinen, Timo; Korpelainen, Eija; Mattila, Kimmo; Pagni, Marco;
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Abstract

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.

Published in

Journal of Applied Crystallography
2009, Volume: 42, number: 3, pages: 376-384

    UKÄ Subject classification

    Bioinformatics (Computational Biology)

    Publication identifier

    DOI: https://doi.org/10.1107/S0021889809008784

    Permanent link to this page (URI)

    https://res.slu.se/id/publ/27187