ArticleProtein science : a publication of the Protein Society2018
Single-particle cryo-EM-Improved ab initio 3D reconstruction with SIMPLE/PRIME.
Article in Protein science : a publication of the Protein Society, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed.
- Article
- Subspace Method of Moments forSIAM journal on imaging sciences · 2026Article
- Probabilistic single-particle cryo-EM ab initio 3D reconstruction in SIMPLE.Acta crystallographica. Section D, Structural biology · 2025Article
- Structural insights into pre-pore intermediates of alpha-hemolysin in the lipidic environment.Nature communications · 2025Article
- Cryo-EM reveals conformational variability in the SARS-CoV-2 spike protein RBD induced by two broadly neutralizing monoclonal antibodies.RSC advances · 2025Article
- Structure and dynamics of GAD65 in complex with an autoimmune polyendocrine syndrome type 2-associated autoantibody.Nature communications · 2025Article
- Time-resolved Brownian tomography of single nanocrystals in liquid during oxidative etching.Nature communications · 2025Article
- Structural insights into the mechanism of protein transport by the Type 9 Secretion System translocon.Nature microbiology · 2024Article
- Cryo-electron microscopy-based drug design.Frontiers in molecular biosciences · 2024Review
- Recognition determinants of improved HIV-1 neutralization by a heavy chain matured pediatric antibody.iScience · 2023Article
- Emerging Themes in CryoEM─Single Particle Analysis Image Processing.Chemical reviews · 2022Review
- Article
- Article
- Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility.Nature microbiology · 2021Article
- Nonameric structures of the cytoplasmic domain of FlhA and SctV in the context of the full-length protein.PloS one · 2021Article
- SINGLE: Atomic-resolution structure identification of nanocrystals by graphene liquid cell EM.Science advances · 2021Article
- Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Determination of the 3D Atomic Structures of Nanoparticles.Small science · 2021Article
- Structures of the stator complex that drives rotation of the bacterial flagellum.Nature microbiology · 2020Article
- Method of moments for 3D single particleInverse problems · 2020Article
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4 authors.
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Abstract
Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. We developed the SIMPLE open-source image-processing suite for analysing cryo-EM images of single-particles. A core component of SIMPLE is the probabilistic PRIME algorithm for identifying clusters of images in 2D and determine relative orientations of single-particle projections in 3D. Here, we extend our previous work on PRIME and introduce new stochastic optimization algorithms that improve the robustness of the approach. Our refined method for identification of homogeneous subsets of images in accurate register substantially improves the resolution of the cluster centers and of the ab initio 3D reconstructions derived from them. We now obtain maps with a resolution better than 10 Å by exclusively processing cluster centers. Excellent parallel code performance on over-the-counter laptops and CPU workstations is demonstrated.
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