Journal
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
Volume 68, Issue -, Pages 484-496Publisher
INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/S0907444911054515
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Funding
- Netherlands Organization for Scientific Research (NWO) [722.011.011]
- Medical Research Council [MC_UP_A025_1012] Funding Source: researchfish
- MRC [MC_UP_A025_1012] Funding Source: UKRI
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Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e. g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R-free and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise 'static' structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets.
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