ArticleJournal of structural biology2022
EMDA: A Python package for Electron Microscopy Data Analysis.
Article in Journal of structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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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
20 citing papers in PubMed, 35 citations in OpenAlex.
- Repositioning of polyubiquitin alters the pathologic tau filament structure.Nature structural & molecular biology · 2026Article
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- The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.Molecular cell · 2025Article
- Uncovering synaptic and cellular nanoarchitecture of brain tissue via seamlessbioRxiv : the preprint server for biology · 2025Article
- Structural basis of anticancer drug recognition and amino acid transport by LAT1.Nature communications · 2025Article
- Computational analyses of drug resistance mutations in katG and emb complexes in Mycobacterium tuberculosis.Proteins · 2025Article
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- Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.Nature methods · 2024Article
- The open gate of the AMPA receptor forms a CaNature structural & molecular biology · 2024Article
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- Article
- Accurate magnification determination for cryoEM using gold.Ultramicroscopy · 2024Article
- Architecture of the biofilm-associated archaic Chaperone-Usher pilus CupE from Pseudomonas aeruginosa.PLoS pathogens · 2023Article
- Overview and applications of map and model validation tools in the CCP-EM software suite.Faraday discussions · 2022Review
- Molecular asymmetry of a photosynthetic supercomplex from green sulfur bacteria.Nature communications · 2022Article
- Article
- Cryo-electron Microscopy of Adeno-associated Virus.Chemical reviews · 2022Review
- A molecular prior distribution for Bayesian inference based on Wilson statistics.Computer methods and programs in biomedicine · 2022Article
- Validation analysis of EMDB entries.Acta crystallographica. Section D, Structural biology · 2022Article
- Assessing the Mobility of Severe Acute Respiratory Syndrome Coronavirus-2 Spike Protein Glycans by Structural and Computational Methods.Frontiers in microbiology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
An open-source Python library EMDA for cryo-EM map and model manipulation is presented with a specific focus on validation. The use of several functionalities in the library is presented through several examples. The utility of local correlation as a metric for identifying map-model differences and unmodeled regions in maps, and how it is used as a metric of map-model validation is demonstrated. The mapping of local correlation to individual atoms, and its use to draw insights on local signal variations are discussed. EMDA's likelihood-based map overlay is demonstrated by carrying out a superposition of two domains in two related structures. The overlay is carried out first to bring both maps into the same coordinate frame and then to estimate the relative movement of domains. Finally, the map magnification refinement in EMDA is presented with an example to highlight the importance of adjusting the map magnification in structural comparison studies.
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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.