ArticleNature methods2023
nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Acoustofluidic cryo-EM enables in situ particle manipulation for uniform, high-quality cryo-EM specimens.Science advances · 2026Article
- CoCryoViS: Collaborative online cryo-electron tomography visualization system.Protein science : a publication of the Protein Society · 2026Article
- FlyTomo: a streamlined software for on-the-fly cryo-ET data processing and diagnosis.Nature communications · 2026Article
- Mechanistic and antigenic boundaries of Henipavirus and Parahenipavirus glycoproteins.Nature communications · 2026Article
- prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation.Structure (London, England : 1993) · 2026Article
- AreTomoLive: automated reconstruction of comprehensively corrected and denoised cryo-electron tomograms in real time and at high throughput.Nature methods · 2026Article
- Article
- A robust workflow for 3D imaging of human mitochondria using cryo-electron tomography.bioRxiv : the preprint server for biology · 2026Article
- In situ structure determination of conformationally flexible targets using nextPYP.Nature protocols · 2026Review
- Resolving structural heterogeneity in situ through cryogenic electron tomography.Current opinion in structural biology · 2026Review
- PhaseT3M: 3D imaging at 1.6 Å resolution via electron cryo-tomography with nonlinear phase retrieval.Nature communications · 2025Article
- Strategies for studying discrete heterogeneity in situ using cryo-electron tomography.Current opinion in structural biology · 2025Review
- Advances in automation for cryo-electron tomography data collection.Current opinion in structural biology · 2025Review
- Distinct Target Site of Lenacapavir in Immature HIV-1 and Concurrent Binding with the Maturation Inhibitor Bevirimat.Journal of the American Chemical Society · 2025Article
- Localization of macromolecules in crowded cellular cryo-electron tomograms from extremely sparse labels.Briefings in bioinformatics · 2025Article
- Cryo-EM single-particle analysis expanding towards increasingly native samples.Acta crystallographica. Section D, Structural biology · 2025Review
- A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries.Current opinion in structural biology · 2025Review
- TomoScore: A Neural Network Approach for Quality Assessment of Cellular cryo-ET.Research square · 2025Article
- Unraveling atomic complexity from frozen samples.Structural dynamics (Melville, N.Y.) · 2025Article
- Cost-benefit analysis of cryogenic electron tomography subtomogram averaging of chaperonin MmCpn at near atomic resolution.Structure (London, England : 1993) · 2025Article
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9 authors.
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Abstract
Single-particle cryo-electron tomography is an emerging technique capable of determining the structure of proteins imaged within the native context of cells at molecular resolution. While high-throughput techniques for sample preparation and tilt-series acquisition are beginning to provide sufficient data to allow structural studies of proteins at physiological concentrations, the complex data analysis pipeline and the demanding storage and computational requirements pose major barriers for the development and broader adoption of this technology. Here, we present a scalable, end-to-end framework for single-particle cryo-electron tomography data analysis from on-the-fly pre-processing of tilt series to high-resolution refinement and classification, which allows efficient analysis and visualization of datasets with hundreds of tilt series and hundreds of thousands of particles. We validate our approach using in vitro and cellular datasets, demonstrating its effectiveness at achieving high-resolution and revealing conformational heterogeneity in situ. The framework is made available through an intuitive and easy-to-use computer application, nextPYP ( http://nextpyp.app ).
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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.