ArticleJournal of chemical information and modeling2020
Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit Using Difference Maps.
Article in Journal of chemical information and modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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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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.
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Who cites it
23 citing papers in PubMed, 38 citations in OpenAlex.
- Small-molecule modulation of β-arrestins.Nature · 2026Article
- Article
- Automated model-free analysis of cryo-EM volume ensembles with SIREn.Structure (London, England : 1993) · 2025Article
- Automated model-free analysis of cryo-EM volume ensembles with SIREn.bioRxiv : the preprint server for biology · 2024Article
- Potassium dependent structural changes in the selectivity filter of HERG potassium channels.Nature communications · 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
- Alignment of density maps in Wasserstein distance.Biological imaging · 2024Article
- In-cell structural insight into the stability of sperm microtubule doublet.Cell discovery · 2023Article
- ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.Science advances · 2023Article
- How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM.Journal of structural biology · 2022Article
- Overview and applications of map and model validation tools in the CCP-EM software suite.Faraday discussions · 2022Review
- Cryo-electron Microscopy of Adeno-associated Virus.Chemical reviews · 2022Review
- Cryo-EM reveals mechanisms of angiotensin I-converting enzyme allostery and dimerization.The EMBO journal · 2022Article
- Adeno-associated virus (AAV) cell entry: structural insights.Trends in microbiology · 2022Review
- Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH.Nature structural & molecular biology · 2022Article
- Cryo-EM single-particle structure refinement and map calculation using Servalcat.Acta crystallographica. Section D, Structural biology · 2021Article
- Validation, analysis and annotation of cryo-EM structures.Acta crystallographica. Section D, Structural biology · 2021Article
- Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.Structure (London, England : 1993) · 2021Article
- VESPER: global and local cryo-EM map alignment using local density vectors.Nature communications · 2021Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
Cryogenic electron microscopy (cryo-EM) is a powerful technique for determining structures of multiple conformational or compositional states of macromolecular assemblies involved in cellular processes. Recent technological developments have led to a leap in the resolution of many cryo-EM data sets, making atomic model building more common for data interpretation. We present a method for calculating differences between two cryo-EM maps or a map and a fitted atomic model. The proposed approach works by scaling the maps using amplitude matching in resolution shells. To account for variability in local resolution of cryo-EM data, we include a procedure for local amplitude scaling that enables appropriate scaling of local map contrast. The approach is implemented as a user-friendly tool in the CCP-EM software package. To obtain clean and interpretable differences, we propose a protocol involving steps to process the input maps and output differences. We demonstrate the utility of the method for identifying conformational and compositional differences including ligands. We also highlight the use of difference maps for evaluating atomic model fit in cryo-EM maps.
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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.