ArticleScientific reports2022
Helical Indexing in Real Space.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Visualization of membrane-stabilized SorCS2Journal of structural biology: X · 2026Article
- Nucleocapsid-like cryo-EM structure of influenza B virus.PLoS pathogens · 2026Article
- Intact architectures of myophage phi92 in extended and contracted states.PLoS pathogens · 2026Article
- Helical reconstruction of amyloids in cryoSPARC.Acta crystallographica. Section F, Structural biology communications · 2026Article
- AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network.Nature methods · 2026Article
- Absolute hand determination of glycofibrils from natural sources in cryo-EM.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Validation of helical symmetry parameters in the EMDB.Acta crystallographica. Section D, Structural biology · 2025Article
- Mechanism for Vipp1 spiral formation, ring biogenesis, and membrane repair.Nature structural & molecular biology · 2025Article
- Influenza a virus antiparallel helical nucleocapsid-like pseudo-atomic structure.Nucleic acids research · 2025Article
- Cryo-EM analysis of Pseudomonas phage Pa193 structural components.Communications biology · 2024Article
- Intracellular Ebola virus nucleocapsid assembly revealed by in situ cryo-electron tomography.Cell · 2024Article
- Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission.Developmental cell · 2024Article
- Purification and Cryo-Electron Microscopy Analysis of Bacterial Appendages.Bio-protocol · 2024Article
- Cryo-EM structures of amyloid-β and tau filaments in Down syndrome.Nature structural & molecular biology · 2024Article
- Cryo-EM analysis of Pseudomonas phage Pa193 structural components.Research square · 2024Article
- Helical reconstruction, again.Current opinion in structural biology · 2024Review
- High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers.Nature communications · 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.
Funding
Abstract
Biological structures with helical symmetries of distinct twist, rise, and axial symmetry are abundant and span a wide range of organisms and functions. Performing de novo helical indexing remains challenging because of the steep learning curve involved in Fourier space layer lines. The unknown amount of out-of-plane tilt and the existence of multiple conformations of the helices further complicate indexing. In this work, we introduce a real-space indexing method that leverages the prior knowledge of the tilt and in-plane angles of the helical filaments/tubes, robust ab initio 3D reconstruction capabilities in single particle cryo-EM to obtain asymmetric reconstructions, and automatic indexing of helical parameters directly from the asymmetric density maps. We validated this approach using data from multiple helical structures of distinct helical symmetries, diameters, flexibility, data qualities, and heterogeneous states. The fully automated tool we introduce for real space indexing, HI3D, uses the 2D lattice in the autocorrelation of the cylindrical projection of a 3D density map to identify the helical symmetry. HI3D can often successfully determine the helical parameters of a suboptimal 3D density map, including ab initio single particle asymmetric reconstructions and sub-tomogram averages, with intermediate evidence that can also help assess the map quality. Furthermore, this open-source HI3D is usable independently as a Web application that can be accessed free of installation. With these methods, de novo helical indexing will be significantly more accessible to researchers investigating structures of helical filaments/tubes using cryo-EM.
Indexed as
Identifiers
What OpenQuestion holds
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.