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 , Matthieu [e-mail] Reichstadt (1) , Vincent Breton (1) , I. J.Tickle , G. Vriend

1 LPC - Laboratoire de Physique Corpusculaire - Clermont-Ferrand

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

Mots clés: grid; PDB-REDO

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

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, 2009, 42, pp.376-384. ⟨10.1107/S0021889809008784⟩. ⟨in2p3-00385213⟩