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説明
<jats:p>Developments of the <jats:italic>PDB_REDO</jats:italic> procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. <jats:italic>PDB_REDO</jats:italic> uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (<jats:italic>e.g.</jats:italic> anisotropic, isotropic or overall <jats:italic>B</jats:italic>-factor refinement, TLS model) and to optimize the geometry <jats:italic>versus</jats:italic> data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. <jats:italic>PDB_REDO</jats:italic> 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 <jats:italic>R</jats:italic> <jats:sub>free</jats:sub> and in terms of widely accepted geometric validation criteria. It is concluded that <jats:italic>PDB_REDO</jats:italic> is useful to update the otherwise `static' structures in the PDB to modern crystallographic standards. The publically available <jats:italic>PDB_REDO</jats:italic> database provides better model statistics and contributes to better refinement and validation targets.</jats:p>
収録刊行物
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- Acta Crystallographica Section D Biological Crystallography
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Acta Crystallographica Section D Biological Crystallography 68 (4), 484-496, 2012-03-16
International Union of Crystallography (IUCr)
