ArticleActa crystallographica. Section D, Structural biology2025
Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps.
Article in Acta crystallographica. Section D, Structural biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed.
- DAQplugin: Interactive Deep Learning-Based Validation of Cryo-EM Protein Models in ChimeraX.bioRxiv : the preprint server for biology · 2026Article
- Structural basis of transcription of the hachimoji eight-letter alphabet by E. coli RNA polymerase.Nature communications · 2026Article
- Comparative assessment of crystallographic and cryo-EM models in the Protein Data Bank.FEBS open bio · 2026Article
- Integrative structural analysis of human endosomal NHE6 reveals a lipid-associated gate and disordered C-terminus.Nature communications · 2026Article
- Ribosomal architecture and rRNA modification landscape in the tick-borne parasite Babesia divergens.Nature communications · 2026Article
- A distinct E dimer epitope underlies selective recognition by a protective human West Nile virus antibody.EMBO reports · 2026Article
- The mechanism of biofilm degradation by a detachable tailspike of gene transfer agents.bioRxiv : the preprint server for biology · 2026Article
- Translation initiation by the Kozak mRNA sequence is based on a conformational readout on the ribosome.Nature communications · 2026Article
- Structure of giant kelp Photosystem I-FCP uncovers drivers of antenna evolution across the red lineage.Nature communications · 2026Article
- Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis.Molecular cell · 2026Article
- Structural basis for the transport mechanism and cholesterol modulation of the human proline transporter.Nature communications · 2026Article
- Cryo-EM Analysis in CASP16.Proteins · 2026Article
- DeepSSETracer 2.0: Improved Deep Learning Model Performance for Protein Secondary Structure Segmentation from Cryo-EM Maps.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2025Article
Corrections and comments
- Update of
Authors and funding
9 authors.
Funding
Abstract
Atomic coordinate models are important for the interpretation of 3D maps produced with cryoEM and cryoET (3D electron microscopy; 3DEM). In addition to visual inspection of such maps and models, quantitative metrics can inform about the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, Q-score, was shown to correlate well with the reported resolution of the map for well fitted models. Here, we present new statistical analyses of Q-score based on its application to ∼10 000 maps and models archived in the EMDB (Electron Microscopy Data Bank) and PDB (Protein Data Bank). Further, we introduce two new metrics based on Q-score to represent each map and model relative to all entries in the EMDB and those with similar resolution. We explore through illustrative examples of proteins, nucleic acids and small molecules how Q-scores can indicate whether the atomic coordinates are well fitted to 3DEM maps and also whether some parts of a map may be poorly resolved due to factors such as molecular flexibility, radiation damage and/or conformational heterogeneity. These examples and statistical analyses provide a basis for how Q-scores can be interpreted effectively in order to evaluate 3DEM maps and atomic coordinate models prior to publication and archiving.
Indexed as
Identifiers
What OpenQuestion holds
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.