ArticleBioinformatics (Oxford, England)2020
Automatic local resolution-based sharpening of cryo-EM maps.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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85 citing papers in PubMed.
- Confidence-guided cryo-EM map optimisation with LocScale-2.0.Nature communications · 2026Article
- EMReady2: improvement of cryo-EM and cryo-ET maps by local quality-aware deep learning with Mamba.Nature communications · 2026Article
- TPP-45142-an Anti-HER2 T-cell Engager-Designed for Selective HER2-Low Cancer Immunotherapy.Molecular cancer therapeutics · 2026Article
- Expression, Purification, and Structural Characterization of Membrane Proteins: A Case Study of the ABC Transporter MsbA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Calicivirus assembly and stability are mediated by the N-terminal domain of the capsid protein with the involvement of the viral genome.PLoS pathogens · 2025Article
- Molecular Basis for the Activation ofJournal of the American Chemical Society · 2025Article
- Cryo-EM reveals molecular mechanisms underlying the inhibitory effect of netrin-4 on laminin matrix formation.Nature communications · 2025Article
- Tension-induced suppression of allosteric conformational changes coordinates kinesin-1 stepping.The Journal of cell biology · 2025Article
- De Novo Hydration of Cryo-EM Reconstructions through Molecular Dynamics Simulations of the Excess Chemical Potential.bioRxiv : the preprint server for biology · 2025Article
- Conformational changes in the motor ATPase CpaF facilitate a rotary mechanism of Tad pilus assembly.Nature communications · 2025Article
- CryoTEN: efficiently enhancing cryo-EM density maps using transformers.Bioinformatics (Oxford, England) · 2025Article
- A labeled dataset for AI-based cryo-EM map enhancement.Computational and structural biotechnology journal · 2025Article
- Structural basis for α-tubulin-specific and modification state-dependent glutamylation.Nature chemical biology · 2024Article
- CryoTEN: Efficiently Enhancing Cryo-EM Density Maps Using Transformers.bioRxiv : the preprint server for biology · 2024Article
- Article
- Molecular recognition of an odorant by the murine trace amine-associated receptor TAAR7f.Nature communications · 2024Article
- Cryo-EM unveils kinesin KIF1A's processivity mechanism and the impact of its pathogenic variant P305L.Nature communications · 2024Article
- Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii.Nature communications · 2024Article
- Vimentin filaments integrate low-complexity domains in a complex helical structure.Nature structural & molecular biology · 2024Article
- Structure-guided mutagenesis of OSCAs reveals differential activation to mechanical stimuli.eLife · 2024Article
25 more citing papers are in PubMed but not listed here.
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14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationRecent technological advances and computational developments have allowed the reconstruction of Cryo-Electron Microscopy (cryo-EM) maps at near-atomic resolution. On a typical workflow and once the cryo-EM map has been calculated, a sharpening process is usually performed to enhance map visualization, a step that has proven very important in the key task of structural modeling. However, sharpening approaches, in general, neglects the local quality of the map, which is clearly suboptimal.
resultsHere, a new method for local sharpening of cryo-EM density maps is proposed. The algorithm, named LocalDeblur, is based on a local resolution-guided Wiener restoration approach of the original map. The method is fully automatic and, from the user point of view, virtually parameter-free, without requiring either a starting model or introducing any additional structure factor correction or boosting. Results clearly show a significant impact on map interpretability, greatly helping modeling. In particular, this local sharpening approach is especially suitable for maps that present a broad resolution range, as is often the case for membrane proteins or macromolecules with high flexibility, all of them otherwise very suitable and interesting specimens for cryo-EM. To our knowledge, and leaving out the use of local filters, it represents the first application of local resolution in cryo-EM sharpening. AVAILABILITY AND IMPLEMENTATION: The source code (LocalDeblur) can be found at https://github.com/I2PC/xmipp and can be run using Scipion (http://scipion.cnb.csic.es) (release numbers greater than or equal 1.2.1). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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