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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
keyword : grid PDB-REDO
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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 : Thursday, January 11, 2018 - 6:14:02 AM

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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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