ArticleMethods (San Diego, Calif.)2016
High resolution single particle refinement in EMAN2.1.
Article in Methods (San Diego, Calif.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 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
101 citing papers in PubMed.
- Engineered Cas9 complexes establish an experimentally grounded benchmark for heterogeneous cryoEM reconstruction methods.bioRxiv : the preprint server for biology · 2026Article
- The Open Conformation of CCT: How to Achieve High Resolution Using CryoEM.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Structural insights into scaffold-guided assembly of the Pseudomonas phage D3 capsid.Nature communications · 2025Article
- Broadly potent spike-specific human monoclonal antibodies inhibit SARS-CoV-2 Omicron sub-lineages.Communications biology · 2024Article
- Activation mechanism and novel binding sites of the BKLife science alliance · 2024Article
- Ciliary tip actin dynamics regulate photoreceptor outer segment integrity.Nature communications · 2024Article
- A kinetic model for solving a combination optimization problem in ab-initio Cryo-EM 3D reconstruction.Briefings in bioinformatics · 2024Article
- Improving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models.Nature methods · 2024Article
- Cryo-electron microscopy-based drug design.Frontiers in molecular biosciences · 2024Review
- Application of Monolayer Graphene to Cryo-Electron Microscopy Grids for High-resolution Structure Determination.Journal of visualized experiments : JoVE · 2023Article
- W546 stacking disruption traps the human porphyrin transporter ABCB6 in an outward-facing transient state.Communications biology · 2023Article
- Recognition determinants of improved HIV-1 neutralization by a heavy chain matured pediatric antibody.iScience · 2023Article
- HIV-1 Vpu protein forms stable oligomers in aqueous solution via its transmembrane domain self-association.Scientific reports · 2023Article
- Application of monolayer graphene to cryo-electron microscopy grids for high-resolution structure determination.bioRxiv : the preprint server for biology · 2023Article
- HIV-1 Vpu protein forms stable oligomers in aqueous solution via its transmembrane domain self-association.bioRxiv : the preprint server for biology · 2023Article
- A symmetry mismatch unraveled: How phage HK97 scaffold flexibly accommodates a 12-fold pore at a 5-fold viral capsid vertex.Science advances · 2023Article
- Integrating Molecular Models Into CryoEM Heterogeneity Analysis Using Scalable High-resolution Deep Gaussian Mixture Models.Journal of molecular biology · 2023Article
- High-throughput cryo-ET structural pattern mining by unsupervised deep iterative subtomogram clustering.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- In Vivo Incorporation of Photoproteins into GroEL Chaperonin Retaining Major Structural and Functional Properties.Molecules (Basel, Switzerland) · 2023Article
- Graph identification of proteins in tomograms (GRIP-Tomo).Protein science : a publication of the Protein Society · 2023Article
41 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
EMAN2.1 is a complete image processing suite for quantitative analysis of grayscale images, with a primary focus on transmission electron microscopy, with complete workflows for performing high resolution single particle reconstruction, 2-D and 3-D heterogeneity analysis, random conical tilt reconstruction and subtomogram averaging, among other tasks. In this manuscript we provide the first detailed description of the high resolution single particle analysis pipeline and the philosophy behind its approach to the reconstruction problem. High resolution refinement is a fully automated process, and involves an advanced set of heuristics to select optimal algorithms for each specific refinement task. A gold standard FSC is produced automatically as part of refinement, providing a robust resolution estimate for the final map, and this is used to optimally filter the final CTF phase and amplitude corrected structure. Additional methods are in-place to reduce model bias during refinement, and to permit cross-validation using other computational methods.
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.