ArticleStructure (London, England : 1993)2017
Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive.
Article in Structure (London, England : 1993), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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Who cites it
26 citing papers in PubMed.
- Lysozyme revisited: evaluating models of a reference protein in structural biology.Current research in structural biology · 2026Article
- Comparative assessment of crystallographic and cryo-EM models in the Protein Data Bank.FEBS open bio · 2026Article
- New targets and procedures for validating the valence geometry of nucleic acid structures.Nucleic acids research · 2026Article
- A Critical Look at the Crystal Structures of cAMP-Dependent Protein Kinases.Kinases and phosphatases · 2025Article
- DEKP: a deep learning model for enzyme kinetic parameter prediction based on pretrained models and graph neural networks.Briefings in bioinformatics · 2025Article
- Review
- Errors in structural biology are not the exception.Acta crystallographica. Section D, Structural biology · 2023Article
- Highly potent natural fungicides identified in silico against the cereal killer fungus Magnaporthe oryzae.Scientific reports · 2022Article
- Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.Biomolecules · 2022Review
- Simplified quality assessment for small-molecule ligands in the Protein Data Bank.Structure (London, England : 1993) · 2022Article
- RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.Protein science : a publication of the Protein Society · 2022Article
- Modernized uniform representation of carbohydrate molecules in the Protein Data Bank.Glycobiology · 2021Article
- Crystal structures of Val58Ile tryptophan repressor in a domain-swapped array in the presence and absence of L-tryptophan.Acta crystallographica. Section F, Structural biology communications · 2021Article
- 'International journal of molecular sciences · 2021Article
- Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction.Structure (London, England : 1993) · 2021Review
- Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.Structure (London, England : 1993) · 2021Article
- Synchrotron Radiation as a Tool for Macromolecular X-Ray Crystallography: a XXI Century Perspective.Nuclear instruments & methods in physics research. Section B, Beam interactions with materials and atoms · 2021Article
- On the evolution of the quality of macromolecular models in the PDB.The FEBS journal · 2020Article
- Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank.International journal of molecular sciences · 2020Article
- Impact of the Protein Data Bank on antineoplastic approvals.Drug discovery today · 2020Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Following deployment of an augmented validation system by the Worldwide Protein Data Bank (wwPDB) partnership, the quality of crystal structures entering the PDB has improved. Of significance are improvements in quality measures now prominently displayed in the wwPDB validation report. Comparisons of PDB depositions made before and after introduction of the new reporting system show improvements in quality measures relating to pairwise atom-atom clashes, side-chain torsion angle rotamers, and local agreement between the atomic coordinate structure model and experimental electron density data. These improvements are largely independent of resolution limit and sample molecular weight. No significant improvement in the quality of associated ligands was observed. Principal component analysis revealed that structure quality could be summarized with three measures (Rfree, real-space R factor Z score, and a combined molecular geometry quality metric), which can in turn be reduced to a single overall quality metric readily interpretable by all PDB archive users.
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