ReviewThe FEBS journal2018
Detect, correct, retract: How to manage incorrect structural models.
Review in The FEBS journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
47 citing papers in PubMed.
- Avoiding pitfalls when modelling ligands in macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2026Article
- Scotty: lattice coincidences in the Protein Data Bank.Acta crystallographica. Section D, Structural biology · 2026Article
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- A high-resolution data set of fatty acid-binding protein structures. III. Unexpectedly high occurrence of wrong ligands.Acta crystallographica. Section D, Structural biology · 2025Article
- Molecular Insight into the Recognition of DNA by the DndCDE Complex in DNA Phosphorothioation.International journal of molecular sciences · 2025Article
- Duplicate entries in the Protein Data Bank: how to detect and handle them.Acta crystallographica. Section D, Structural biology · 2025Article
- If you cannot see it, is it still there?Journal of applied crystallography · 2025Article
- Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2.Nucleic acids research · 2025Article
- Ligand identification in CryoEM and X-ray maps using deep learning.Bioinformatics (Oxford, England) · 2024Article
- How Do Gepotidacin and Zoliflodacin Stabilize DNA-Cleavage Complexes with Bacterial Type IIA Topoisomerases? 2. A Single Moving Metal Mechanism.International journal of molecular sciences · 2024Article
- Ligand Identification in CryoEM and X-ray Maps Using Deep Learning.bioRxiv : the preprint server for biology · 2024Article
- How Do Gepotidacin and Zoliflodacin Stabilize DNA Cleavage Complexes with Bacterial Type IIA Topoisomerases? 1. Experimental Definition of Metal Binding Sites.International journal of molecular sciences · 2024Article
- Exploring Novel GSK-3β Inhibitors for Anti-Neuroinflammatory and Neuroprotective Effects: Synthesis, Crystallography, Computational Analysis, and Biological Evaluation.ACS chemical neuroscience · 2024Article
- Article
- InsPection of electron density maps supports wrongly modeled hexakisphosphate (InsP6) bound to African swine fever mRNA-decapping enzyme g5Rp.Journal of virology · 2024Article
- One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse.Nature communications · 2024Article
- MetalHawk: Enhanced Classification of Metal Coordination Geometries by Artificial Neural Networks.Journal of chemical information and modeling · 2024Article
- Metal ions in biomedically relevant macromolecular structures.Frontiers in chemistry · 2024Review
- DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models.Nucleic acids research · 2023Article
- Sequence-assignment validation in protein crystal structure models with checkMySequence.Acta crystallographica. Section D, Structural biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
The massive technical and computational progress of biomolecular crystallography has generated some adverse side effects. Most crystal structure models, produced by crystallographers or well-trained structural biologists, constitute useful sources of information, but occasional extreme outliers remind us that the process of structure determination is not fail-safe. The occurrence of severe errors or gross misinterpretations raises fundamental questions: Why do such aberrations emerge in the first place? How did they evade the sophisticated validation procedures which often produce clear and dire warnings, and why were severe errors not noticed by the depositors themselves, their supervisors, referees and editors? Once detected, what can be done to either correct, improve or eliminate such models? How do incorrect models affect the underlying claims or biomedical hypotheses they were intended, but failed, to support? What is the long-range effect of the propagation of such errors? And finally, what mechanisms can be envisioned to restore the validity of the scientific record and, if necessary, retract publications that are clearly invalidated by the lack of experimental evidence? We suggest that cognitive bias and flawed epistemology are likely at the root of the problem. By using examples from the published literature and from public repositories such as the Protein Data Bank, we provide case summaries to guide correction or improvement of structural models. When strong claims are unsustainable because of a deficient crystallographic model, removal of such a model and even retraction of the affected publication are necessary to restore the integrity of the scientific record.
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Registered trials
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.