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Journal of Applied Crystallography 42 (2009) 376-384
PDB_REDO: automated re-refinement of X-ray structure models in the PDB
R.P. Joosten, J. Salzemann1, V. Bloch1, H. Stockinger, A.-C. Berglund, C. Blanchet, E. Bongcam-Rudloff, C. Combet, A. L. Da Costa1, G. Deleage, M. Diarena1, R. Fabbretti, G. Fettahi1, V. Flegel, A. Gisel, V. Kasam, T. Kervinen, E. Korpelainen, K. Mattila, M. Pagni, M. Reichstadt1, V. Breton1, I. J.Tickle, G. Vriend

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
1 :  LPC - Laboratoire de Physique Corpusculaire [Clermont-Ferrand]

Sciences du Vivant/Bio-Informatique, Biologie Systémique
grid – PDB-REDO