ArticleJournal of structural biology2013
Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.
Article in Journal of structural biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed.
- Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.Frontiers in bioinformatics · 2026Article
- Recognizing amino acid sidechains in a medium-resolution cryo-electron density map.Protein science : a publication of the Protein Society · 2025Article
- Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.Nature methods · 2024Article
- Article
- Article
- EMDB-the Electron Microscopy Data Bank.Nucleic acids research · 2024Review
- Article
- Assessment of three-dimensional RNA structure prediction in CASP15.bioRxiv : the preprint server for biology · 2023Article
- Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future.Biophysical reviews · 2022Review
- Overview and applications of map and model validation tools in the CCP-EM software suite.Faraday discussions · 2022Review
- Validation analysis of EMDB entries.Acta crystallographica. Section D, Structural biology · 2022Article
- Atomic model validation using the CCP-EM software suite.Acta crystallographica. Section D, Structural biology · 2022Article
- Cryo-EM targets in CASP14.Proteins · 2021Article
- Validation, analysis and annotation of cryo-EM structures.Acta crystallographica. Section D, Structural biology · 2021Article
- Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.Nature methods · 2021Article
- Cryo-EM Map-Based Model Validation Using the False Discovery Rate Approach.Frontiers in molecular biosciences · 2021Article
- Evolving data standards for cryo-EM structures.Structural dynamics (Melville, N.Y.) · 2020Article
- ETDB-Caltech: A blockchain-based distributed public database for electron tomography.PloS one · 2019Article
- Structural biology data archiving - where we are and what lies ahead.FEBS letters · 2018Review
- Real-space refinement in PHENIX for cryo-EM and crystallography.Acta crystallographica. Section D, Structural biology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed.
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.