ArticleActa crystallographica. Section D, Structural biology2021
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models.
Article in Acta crystallographica. Section D, Structural biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.Journal of chemical information and modeling · 2026Article
- New targets and procedures for validating the valence geometry of nucleic acid structures.Nucleic acids research · 2026Article
- AQuaRef: machine learning accelerated quantum refinement of protein structures.Nature communications · 2025Article
- KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.bioRxiv : the preprint server for biology · 2025Article
- gapTrick-structural characterization of protein-protein interactions using AlphaFold.Bioinformatics (Oxford, England) · 2025Article
- Advances in cryo-electron microscopy (cryoEM) for structure-based drug discovery.Expert opinion on drug discovery · 2025Review
- 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
- Predicting Inhibition of CDK2 with SAnDReS: The Application of Machine Learning to Navigate the Scoring Function Space.Current medicinal chemistry · 2025Review
- Cryo-EM structure and B-factor refinement with ensemble representation.Nature communications · 2024Article
- Autoregulation of the LIM kinases by their PDZ domain.Nature communications · 2023Article
- Computational methods forFrontiers in cellular and infection microbiology · 2023Review
- Using deep-learning predictions of inter-residue distances for model validation.Acta crystallographica. Section D, Structural biology · 2022Article
- Overview and applications of map and model validation tools in the CCP-EM software suite.Faraday discussions · 2022Review
- Sequence-assignment validation in cryo-EM models with checkMySequence.Acta crystallographica. Section D, Structural biology · 2022Article
- Atomic model validation using the CCP-EM software suite.Acta crystallographica. Section D, Structural biology · 2022Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM structures and how they might be improved, models deposited in the Protein Data Bank that have map resolutions of better than 5 Å were automatically re-refined using current versions of Phenix tools. The results are available on a publicly accessible web page (https://cci.lbl.gov/ceres). The implementation of a Cryo-EM Re-refinement System (CERES) for the improvement of models deposited in the wwPDB, and the results of the re-refinements, are described. Based on these results, contents are proposed for a `cryo-EM Table 1', which summarizes experimental details and validation metrics in a similar way to `Table 1' in crystallography. The consistent use of robust metrics for the evaluation of cryo-EM models and data should accompany every structure deposition and be reported in scientific publications.
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.