ArticleJournal of structural biology2018
Building atomic models based on near atomic resolution cryoEM maps with existing tools.
Article in Journal of structural biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed, 20 citations in OpenAlex.
- Structural choreography of bacteriophage N4 ejection proteins and the giant virion-associated RNA polymerase.Nature communications · 2026Article
- Structure of the giant RNA polymerase ejected from coliphage N4.Research square · 2025Article
- CryoEM structure of thebioRxiv : the preprint server for biology · 2025Article
- Structures of Native Doublet Microtubules from Trichomonas vaginalis Reveal Parasite-Specific Proteins.Nature communications · 2025Article
- Single Acetylation-mimetic Mutation in TDP-43 Nuclear Localization Signal Disrupts Importin α1/β Signaling.Journal of molecular biology · 2024Article
- Structures of Native Doublet Microtubules fromResearch square · 2024Article
- Apolipoprotein E secreted by astrocytes forms antiparallel dimers in discoidal lipoproteins.Neuron · 2024Article
- Multiple conformations of trimeric spikes visualized on a non-enveloped virus.Nature communications · 2022Article
- Asymmetric reconstruction of mammalian reovirus reveals interactions among RNA, transcriptional factor µ2 and capsid proteins.Nature communications · 2021Article
- Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus.Nature microbiology · 2020Article
- Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps.Journal of chemical information and modeling · 2020Article
- Genome organization and interaction with capsid protein in a multipartite RNA virus.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Conservative transcription in three steps visualized in a double-stranded RNA virus.Nature structural & molecular biology · 2019Article
- DNA-Packing Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus KSHV.Cell · 2019Article
- In situ structures of RNA-dependent RNA polymerase inside bluetongue virus before and after uncoating.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Comparing cryo-EM structures.Journal of structural biology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
The EMDataBank Validation Challenge was a challenging task for students newly introduced to the cryoEM and molecular modeling fields. However, the competition provided an effective space for student modelers to discover and explore the potentials of atomic modeling and refinement by practicing on published atomic structures. Here, by employing manual molecular modeling programs such as Coot, Phenix, and Chimera, we have regularized and improved three targets. The T20S proteasome and TRPV1 ion channel allowed us to broaden our understanding of these modeling techniques while the 70S ribosome served as a challenge to test the limits of our abilities. We were successful in our efforts to improve each of the models and provide here our cohesive methodology for de novo modeling with and without homology models, which may serve as a starting point for other undergraduates and researchers just entering the realm of cryoEM. Additionally, we provide some constructive criticism to facilitate the introduction of said undergraduates and researchers into cryoEM in the future.
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.