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Journal articles
PDB_REDO: automated re-refinement of X-ray structure models in the PDB
R.P. Joosten
J. Salzemann
1
V. Bloch
1
H. Stockinger
A.-C. Berglund
Christophe Blanchet
E. Bongcam-Rudloff
C. Combet
A.L. da Costa
1
G. Deleage
M. Diarena
1
R. Fabbretti
G. Fettahi
1
V. Flegel
A. Gisel
V. Kasam
T. Kervinen
E. Korpelainen
K. Mattila
M. Pagni
M. Reichstadt
1
Vincent Breton
1
I. J.Tickle
G. Vriend
M. Reichstadt 1
Author IdHAL : mreichstadt ORCID : https://orcid.org/0000-0001-7311-2247
Vincent Breton 1
Author
I. J.Tickle
Author
G. Vriend
Author
1
LPC - Laboratoire de Physique Corpusculaire - Clermont-Ferrand (Campus des Cézeaux, 24 avenue des Landais, BP 80026, 63171 Aubière Cedex - France)
- UBP - Université Blaise Pascal - Clermont-Ferrand 2 (34, avenue Carnot - BP 185 / 63006 Clermont-Ferrand cedex - France)
- IN2P3 - Institut National de Physique Nucléaire et de Physique des Particules du CNRS (France)
- CNRS - Centre National de la Recherche Scientifique : UMR6533 (France)
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
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Journal articles
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http://hal.in2p3.fr/in2p3-00385213
Contributor : Jeanine Pellet <>
Submitted on : Monday, May 18, 2009 - 4:13:44 PM
Last modification on : Monday, June 21, 2021 - 5:20:02 PM
Contributor : Jeanine Pellet <>
Submitted on : Monday, May 18, 2009 - 4:13:44 PM
Last modification on : Monday, June 21, 2021 - 5:20:02 PM
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- HAL Id : in2p3-00385213, version 1
- DOI : 10.1107/S0021889809008784
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IN2P3 | LPC-CLERMONT | CNRS | PRES_CLERMONT
Citation
R.P. Joosten, J. Salzemann, V. Bloch, H. Stockinger, A.-C. Berglund, et al.. PDB_REDO: automated re-refinement of X-ray structure models in the PDB. Journal of Applied Crystallography, International Union of Crystallography, 2009, 42, pp.376-384. ⟨10.1107/S0021889809008784⟩. ⟨in2p3-00385213⟩
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