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

Robbie P. Joosten; Jean Salzemann; Vincent Bloch; Heinz Stockinger; Ann-Charlott Berglund; Christophe Blanchet; Erik Bongcam-Rudloff; Christophe Combet; Ana L. Da Costa; Gilbert Deleage; Matteo Diarena; Roberto Fabbretti; Geraldine Fettahi; Volker Flegel; Andreas Gisel; Vinod Kasam; Timo Kervinen; Eija Korpelainen; Kimmo Mattila; Marco Pagni; Matthieu Reichstadt; Vincent Breton; Ian J. Tickle; Gert Vriend

doi:10.1107/S0021889809008784

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

Robbie P. Joosten
, Jean Salzemann
, Vincent Bloch
, Heinz Stockinger
, Ann-Charlott Berglund
, Christophe Blanchet
, Erik Bongcam-Rudloff
, Christophe Combet
, Ana L. Da Costa
, Gilbert Deleage
, Matteo Diarena
, Roberto Fabbretti
, Geraldine Fettahi
, Volker Flegel
, Andreas Gisel
, Vinod Kasam
, Timo Kervinen
, Eija Korpelainen
, Kimmo Mattila
, Marco Pagni

Matthieu Reichstadt, Vincent Breton, Ian J. Tickle, Gert Vriend

Publikation: Bidrag till tidskrift › Artikel i vetenskaplig tidskrift › Peer review

Sammanfattning

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.

Originalspråk	Engelska
Sidor (från-till)	376-384
Antal sidor	9
Tidskrift	Journal of Applied Crystallography
Volym	42
Nummer	3
DOI	https://doi.org/10.1107/S0021889809008784
Status	Publicerad - 2009
Externt publicerad	Ja

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10.1107/S0021889809008784

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Joosten, R. P., Salzemann, J., Bloch, V., Stockinger, H., Berglund, A.-C., Blanchet, C., Bongcam-Rudloff, E., Combet, C., Da Costa, A. L., Deleage, G., Diarena, M., Fabbretti, R., Fettahi, G., Flegel, V., Gisel, A., Kasam, V., Kervinen, T., Korpelainen, E., Mattila, K., ... Vriend, G. (2009). PDB_REDO: automated re-refinement of X-ray structure models in the PDB. Journal of Applied Crystallography, 42(3), 376-384. https://doi.org/10.1107/S0021889809008784

@article{2b61e7f4cf6544718f89e3dadf47310c,

title = "PDB\_REDO: automated re-refinement of X-ray structure models in the PDB",

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.",

author = "Joosten, \{Robbie P.\} and Jean Salzemann and Vincent Bloch and Heinz Stockinger and Ann-Charlott Berglund and Christophe Blanchet and Erik Bongcam-Rudloff and Christophe Combet and \{Da Costa\}, \{Ana L.\} and Gilbert Deleage and Matteo Diarena and Roberto Fabbretti and Geraldine Fettahi and Volker Flegel and Andreas Gisel and Vinod Kasam and Timo Kervinen and Eija Korpelainen and Kimmo Mattila and Marco Pagni and Matthieu Reichstadt and Vincent Breton and Tickle, \{Ian J.\} and Gert Vriend",

year = "2009",

doi = "10.1107/S0021889809008784",

language = "English",

volume = "42",

pages = "376--384",

journal = "Journal of Applied Crystallography",

issn = "0021-8898",

publisher = "International Union of Crystallography",

number = "3",

}

Joosten, RP, Salzemann, J, Bloch, V, Stockinger, H, Berglund, A-C, Blanchet, C, Bongcam-Rudloff, E, Combet, C, Da Costa, AL, Deleage, G, Diarena, M, Fabbretti, R, Fettahi, G, Flegel, V, Gisel, A, Kasam, V, Kervinen, T, Korpelainen, E, Mattila, K, Pagni, M, Reichstadt, M, Breton, V, Tickle, IJ & Vriend, G 2009, 'PDB_REDO: automated re-refinement of X-ray structure models in the PDB', Journal of Applied Crystallography, vol. 42, nr. 3, s. 376-384. https://doi.org/10.1107/S0021889809008784

TY - JOUR

T1 - PDB_REDO: automated re-refinement of X-ray structure models in the PDB

AU - Joosten, Robbie P.

AU - Salzemann, Jean

AU - Bloch, Vincent

AU - Stockinger, Heinz

AU - Berglund, Ann-Charlott

AU - Blanchet, Christophe

AU - Bongcam-Rudloff, Erik

AU - Combet, Christophe

AU - Da Costa, Ana L.

AU - Deleage, Gilbert

AU - Diarena, Matteo

AU - Fabbretti, Roberto

AU - Fettahi, Geraldine

AU - Flegel, Volker

AU - Gisel, Andreas

AU - Kasam, Vinod

AU - Kervinen, Timo

AU - Korpelainen, Eija

AU - Mattila, Kimmo

AU - Pagni, Marco

AU - Reichstadt, Matthieu

AU - Breton, Vincent

AU - Tickle, Ian J.

AU - Vriend, Gert

PY - 2009

Y1 - 2009

N2 - 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.

AB - 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.

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

U2 - 10.1107/S0021889809008784

DO - 10.1107/S0021889809008784

M3 - Journal article

SN - 0021-8898

VL - 42

SP - 376

EP - 384

JO - Journal of Applied Crystallography

JF - Journal of Applied Crystallography

IS - 3

ER -