ReviewProgress in biophysics and molecular biology2021
Tools for visualizing and analyzing Fourier space sampling in Cryo-EM.
Review in Progress in biophysics and molecular biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Structural Mechanism of Filamentation Induced Dampening of GTP Inhibition of Glutamate Dehydrogenase.bioRxiv : the preprint server for biology · 2026Article
- Diversifying particle-orientation distributions in cryo-EM with LEA protein additives.bioRxiv : the preprint server for biology · 2026Article
- Structures of asymmetric particles of tick-borne encephalitis virus provide insight into flavivirus assembly and maturation.Science advances · 2026Article
- prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation.Structure (London, England : 1993) · 2026Article
- Engineered Cas9 complexes establish an experimentally grounded benchmark for heterogeneous cryoEM reconstruction methods.bioRxiv : the preprint server for biology · 2026Article
- Structural flexibility of the human vault particle revealed by high-resolution cryo-EM and molecular dynamics simulations.Nature communications · 2026Article
- Scaffolds with optimized quaternary symmetry for de novo cryoEM structure determination of small RNAs.Nature methods · 2026Article
- Explicit correction of severely non-uniform distributions of cryo-EM views.Acta crystallographica. Section D, Structural biology · 2026Article
- Ultrathin liquid cells for microsecond time-resolved cryo-EM.Nature communications · 2026Article
- Cryo-EM structure of the human COP1-DET1 ubiquitin ligase complex.Nature communications · 2026Article
- Antibodies disrupt bacterial adhesion by ligand mimicry and allosteric interference.Nature communications · 2025Article
- Commensal gut bacteria employ de-chelatase HmuS to harvest iron from heme.The EMBO journal · 2025Article
- Oligomeric HIV-1 integrase structures reveal functional plasticity for intasome assembly and RNA binding.Nature communications · 2025Article
- Laser flash melting cryo-EM samples to overcome preferred orientation.Nature methods · 2025Article
- Cryo-EM reveals molecular mechanisms underlying the inhibitory effect of netrin-4 on laminin matrix formation.Nature communications · 2025Article
- CryoPROS: Correcting misalignment caused by preferred orientation using AI-generated auxiliary particles.Nature communications · 2025Article
- Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.Nature communications · 2024Article
- Article
- Two-metal ion mechanism of DNA cleavage by activated, filamentous SgrAI.The Journal of biological chemistry · 2024Article
- Correction of preferred orientation-induced distortion in cryo-electron microscopy maps.Science advances · 2024Article
Corrections and comments
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Authors and funding
2 authors.
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Abstract
A complete understanding of how an orientation distribution contributes to a cryo-EM reconstruction remains lacking. It is necessary to begin critically assessing the set of views to gain an understanding of its effect on experimental reconstructions. Toward that end, we recently suggested that the type of orientation distribution may alter resolution measures in a systematic manner. We introduced the sampling compensation factor (SCF), which incorporates how the collection geometry might change the spectral signal-to-noise ratio (SSNR), irrespective of the other experimental aspects. We show here that knowledge of the sampling restricted to spherical surfaces of sufficiently large radii in Fourier space is equivalent to knowledge of the set of projection views. Moreover, the SCF geometrical factor may be calculated from one such surface. To aid cryo-EM practitioners, we developed a graphical user interface (GUI) tool that evaluates experimental orientation distributions. The GUI returns plots of projection directions, sampling constrained to the surface of a sphere, the SCF value, the fraction of the empty region of Fourier space, and a histogram of the sampling values over the points on a sphere. Finally, a fixed tilt angle may be incorporated to determine how tilting the grid during collection may improve the distribution of views and Fourier space sampling. We advocate this simple conception of sampling and the use of such tools as a complement to the distribution of views to capture the different aspects of the effect of projection directions on cryo-EM reconstructions.
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