ArticleActa crystallographica. Section D, Biological crystallography2012
PDB_REDO: constructive validation, more than just looking for errors.
Article in Acta crystallographica. Section D, Biological crystallography, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 134 papers.
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134 citing papers in PubMed.
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- SadB, a mediator of AmrZ proteolysis and biofilm development in Pseudomonas aeruginosa.NPJ biofilms and microbiomes · 2025Article
- Filamin C dimerisation is regulated by HSPB7.Nature communications · 2025Article
- Peptide bonds strike back.IUCrJ · 2025Article
- Duplicate entries in the Protein Data Bank: how to detect and handle them.Acta crystallographica. Section D, Structural biology · 2025Article
- Molecular glues of the regulatory ChREBP/14-3-3 complex protect beta cells from glucolipotoxicity.Nature communications · 2025Article
- Viral sequence determines HLA-E-restricted T cell recognition of hepatitis B surface antigen.Nature communications · 2024Article
- Molecular glues of the regulatory ChREBP/14-3-3 complex protect beta cells from glucolipotoxicity.bioRxiv : the preprint server for biology · 2024Article
- Using deep-learning predictions reveals a large number of register errors in PDB depositions.IUCrJ · 2024Article
- Robust and automatic beamstop shadow outlier rejection: combining crystallographic statistics with modern clustering under a semi-supervised learning strategy.Acta crystallographica. Section D, Structural biology · 2024Article
- MUT-7 exoribonuclease activity and localization are mediated by an ancient domain.Nucleic acids research · 2024Article
- Exploring the sequence-function space of microbial fucosidases.Communications chemistry · 2024Article
74 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
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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