ArticleJournal of structural biology2017
Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.
Article in Journal of structural biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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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
42 citing papers in PubMed, 69 citations in OpenAlex.
- Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.Frontiers in bioinformatics · 2026Article
- In-cell structure and variability of pyrenoid Rubisco.Nature communications · 2025Article
- Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps.Acta crystallographica. Section D, Structural biology · 2025Article
- CryoAlign2: efficient global and local Cryo-EM map retrieval based on parallel-accelerated local spatial structural features.Bioinformatics (Oxford, England) · 2025Article
- Slice'N'Dice: maximizing the value of predicted models for structural biologists.Acta crystallographica. Section D, Structural biology · 2025Article
- Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method.Scientific reports · 2024Article
- Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.Nature methods · 2024Article
- Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference.PLoS computational biology · 2024Article
- Accurate global and local 3D alignment of cryo-EM density maps using local spatial structural features.Nature communications · 2024Article
- ChemEM: Flexible Docking of Small Molecules in Cryo-EM Structures.Journal of medicinal chemistry · 2024Article
- Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15.Proteins · 2023Article
- Article
- Assessment of three-dimensional RNA structure prediction in CASP15.bioRxiv : the preprint server for biology · 2023Article
- Likelihood-based signal and noise analysis for docking of models into cryo-EM maps.Acta crystallographica. Section D, Structural biology · 2023Article
- Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score.Acta crystallographica. Section D, Structural 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
- Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly.Nature communications · 2022Article
- 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
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Recent developments in 3-dimensional electron microcopy (3D-EM) techniques and a concomitant drive to look at complex molecular structures, have led to a rapid increase in the amount of volume data available for biomolecules. This creates a demand for better methods to analyse the data, including improved scores for comparison, classification and integration of data at different resolutions. To this end, we developed and evaluated a set of scoring functions that compare 3D-EM volumes. To test our scores we used a benchmark set of volume alignments derived from the Electron Microscopy Data Bank. We find that the performance of different scores vary with the map-type, resolution and the extent of overlap between volumes. Importantly, adding the overlap information to the local scoring functions can significantly improve their precision and accuracy in a range of resolutions. A combined score involving the local mutual information and overlap (LMI_OV) performs best overall, irrespective of the map category, resolution or the extent of overlap, and we recommend this score for general use. The local mutual information score itself is found to be more discriminatory than cross-correlation coefficient for intermediate-to-low resolution maps or when the map size and density distribution differ significantly. For comparing map surfaces, we implemented two filters to detect the surface points, including one based on the 'extent of surface exposure'. We show that scores that compare surfaces are useful at low resolutions and for maps with evident surface features. All the scores discussed are implemented in TEMPy (http://tempy.ismb.lon.ac.uk/).
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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.