ArticleActa crystallographica. Section D, Biological crystallography2012
Implementing an X-ray validation pipeline for the Protein Data Bank.
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 71 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
71 citing papers in PubMed.
- IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank.Journal of molecular biology · 2026Article
- Ribosomal RNA cleavage by the previously unidentified RelS-RelI toxin-antitoxin system controls growth of Mycobacterium tuberculosis.Nucleic acids research · 2026Article
- Exploration of questionable backbone conformations in crystallographic structure models using a structural alphabet.Acta crystallographica. Section D, Structural biology · 2025Article
- Ribonuclease toxin RelE1 inhibits growth of Mycobacterium tuberculosis through specific cleavage of the ribosomal anti-Shine-Dalgarno region.Nucleic acids research · 2025Article
- Semi-automated modeling of reaction states in time-resolved serial femtosecond crystallography using molecular dynamics sampled conformations.Structural dynamics (Melville, N.Y.) · 2025Article
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- Toxin release by conditional remodelling of ParDE1 from Mycobacterium tuberculosis leads to gyrase inhibition.Nucleic acids research · 2024Article
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- The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3.Communications biology · 2023Article
- MenT nucleotidyltransferase toxins extend tRNA acceptor stems and can be inhibited by asymmetrical antitoxin binding.Nature communications · 2023Article
- The CCP4 suite: integrative software for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- Dephosphocholination by Legionella effector Lem3 functions through remodelling of the switch II region of Rab1b.Nature communications · 2023Article
- Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.The journal of physical chemistry. B · 2022Article
- Simplified quality assessment for small-molecule ligands in the Protein Data Bank.Structure (London, England : 1993) · 2022Article
- Experiences From Developing Software for Large X-Ray Crystallography-Driven Protein-Ligand Studies.Frontiers in molecular biosciences · 2022Article
- Crystal structure of the BREX phage defence protein BrxA.Current research in structural biology · 2022Article
- Crystal structure of the anti-CRISPR repressor Aca2.Journal of structural biology · 2021Article
- Antitoxin autoregulation of M. tuberculosis toxin-antitoxin expression through negative cooperativity arising from multiple inverted repeat sequences.The Biochemical journal · 2020Article
- SASBDB: Towards an automatically curated and validated repository for biological scattering data.Protein science : a publication of the Protein Society · 2020Article
- New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics.Protein science : a publication of the Protein Society · 2020Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
There is an increasing realisation that the quality of the biomacromolecular structures deposited in the Protein Data Bank (PDB) archive needs to be assessed critically using established and powerful validation methods. The Worldwide Protein Data Bank (wwPDB) organization has convened several Validation Task Forces (VTFs) to advise on the methods and standards that should be used to validate all of the entries already in the PDB as well as all structures that will be deposited in the future. The recommendations of the X-ray VTF are currently being implemented in a software pipeline. Here, ongoing work on this pipeline is briefly described as well as ways in which validation-related information could be presented to users of structural data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.