ArticleMethods (San Diego, Calif.)2016
Methods to account for movement and flexibility in cryo-EM data processing.
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. An erratum has been issued. Cited by 16 papers.
What it found
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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.
- Structural Biology for Target Identification and Validation.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Mitigating the Blurring Effect of CryoEM Averaging on a Flexible and Highly Symmetric Protein Complex through Sub-Particle Reconstruction.International journal of molecular sciences · 2024Article
- A large expert-curated cryo-EM image dataset for machine learning protein particle picking.Scientific data · 2023Article
- CryoPPP: A Large Expert-Labelled Cryo-EM Image Dataset for Machine Learning Protein Particle Picking.bioRxiv : the preprint server for biology · 2023Article
- Article
- Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity.Biomolecules · 2022Review
- Comparative Immunogenicity of Bacterially Expressed Soluble Trimers and Nanoparticle Displayed Influenza Hemagglutinin Stem Immunogens.Frontiers in immunology · 2022Article
- Cryo-EM as a powerful tool for drug discovery: recent structural based studies of SARS-CoV-2.Applied microscopy · 2021Review
- Hands on Methods for High Resolution Cryo-Electron Microscopy Structures of Heterogeneous Macromolecular Complexes.Frontiers in molecular biosciences · 2019Review
- Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.Acta crystallographica. Section F, Structural biology communications · 2019Review
- Approaches to altering particle distributions in cryo-electron microscopy sample preparation.Acta crystallographica. Section D, Structural biology · 2018Review
- Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.eLife · 2017Article
- Structural Study of Heterogeneous Biological Samples by Cryoelectron Microscopy and Image Processing.BioMed research international · 2017Review
- Structural analysis of X-linked retinoschisis mutations reveals distinct classes which differentially effect retinoschisin function.Human molecular genetics · 2016Article
- The changing landscape of membrane protein structural biology through developments in electron microscopy.Molecular membrane biology · 2016Review
- Identifying and Visualizing Macromolecular Flexibility in Structural Biology.Frontiers in molecular biosciences · 2016Review
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
Abstract
Recent advances in direct electron detectors and improved CMOS cameras have been accompanied by the development of a range of software to take advantage of the data they produce. In particular they allow for the correction of two types of motion in cryo electron microscopy samples: motion correction for movements of the sample particles in the ice, and differential masking to account for heterogeneity caused by flexibility within protein complexes. Here we provide several scripts that allow users to move between RELION and standalone motion correction and centring programs. We then compare the computational cost and improvements in data quality with each program. We also describe our masking procedures to account for conformational flexibility. For the different elements of this study we have used three samples; a high symmetry virus, flexible protein complex (∼1MDa) and a relatively small protein complex (∼550kDa), to benchmark four widely available motion correction packages. Using these as test cases we demonstrate how motion correction and differential masking, as well as an additional particle re-centring protocol can improve final reconstructions when used within the RELION image-processing package.
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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.