ArticleScientific reports2017
EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 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
32 citing papers in PubMed.
- F-Type Pyocin Versus Phage λ Tail: Conserved Hub, Divergent Fibers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A trimeric architecture reveals the glucitol PTS transporter as a distinct superfamily.Communications biology · 2026Article
- Structural basis for the extended-spectrum antimicrobial activity of Garvieacin Q.Applied and environmental microbiology · 2026Article
- CryoEM and computational modeling structural insights into the pH regulator NBCn1.Nature communications · 2025Article
- Cryo-EM structure of the human MON1A-CCZ1-RAB7A complex provides insights into nucleotide exchange mechanism.Life metabolism · 2025Article
- Structure of an F-type phage tail-like bacteriocin from Listeria monocytogenes.Nature communications · 2025Article
- A pan-orthoebolavirus neutralizing antibody encoded by mRNA effectively prevents virus infection.Emerging microbes & infections · 2024Article
- Structural mechanism of bacteriophage lambda tail's interaction with the bacterial receptor.Nature communications · 2024Article
- Structural morphing in the viral portal vertex of bacteriophage lambda.Journal of virology · 2024Article
- Structural Basis of the Mechanisms of Action and Immunity of Lactococcin A, a Class IId Bacteriocin.Applied and environmental microbiology · 2023Article
- Article
- Structural Basis of Pore Formation in the Mannose Phosphotransferase System by Pediocin PA-1.Applied and environmental microbiology · 2022Article
- Cryo-EM structure of the sodium-driven chloride/bicarbonate exchanger NDCBE.Nature communications · 2021Article
- The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP.Acta crystallographica. Section D, Structural biology · 2021Article
- Structures of human dual oxidase 1 complex in low-calcium and high-calcium states.Nature communications · 2021Article
- Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state.Nature structural & molecular biology · 2020Article
- Cryo-electron Microscopy Structure of the Swine Acute Diarrhea Syndrome Coronavirus Spike Glycoprotein Provides Insights into Evolution of Unique Coronavirus Spike Proteins.Journal of virology · 2020Article
- Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM.Acta crystallographica. Section D, Structural biology · 2020Article
- Structural insights into sodium transport by the oxaloacetate decarboxylase sodium pump.eLife · 2020Article
- Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy.Journal of chemical information and modeling · 2020Review
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
No grant is acknowledged in the PubMed record.
Abstract
The resolution of electron-potential maps in single-particle cryo-electron microscopy (cryoEM) is approaching atomic or near- atomic resolution. However, no program currently exists for de novo cryoEM model building at resolutions exceeding beyond 3.5 Å. Here, we present a program, EMBuilder, based on template matching, to generate cryoEM models at high resolution. The program identifies features in both secondary-structure and Cα stages. In the secondary structure stage, helices and strands are identified with pre-computed templates, and the voxel size of the entire map is then refined to account for microscopic magnification errors. The identified secondary structures are then extended from both ends in the Cα stage via a log-likelihood (LLK) target function, and if possible, the side chains are also assigned. This program can build models of large proteins (~1 MDa) in a reasonable amount of time (~1 day) and thus has the potential to greatly decrease the manual workload required for model building of high-resolution cryoEM maps.
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.