ArticleBiophysical journal2016
StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.
Article in Biophysical journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- How many (distinguishable) classes can we identify in single-particle analysis?Acta crystallographica. Section D, Structural biology · 2025Article
- Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing.International journal of molecular sciences · 2023Article
- Methods for Cryo-EM Single Particle Reconstruction of Macromolecules Having Continuous Heterogeneity.Journal of molecular biology · 2023Review
- Integrating Molecular Models Into CryoEM Heterogeneity Analysis Using Scalable High-resolution Deep Gaussian Mixture Models.Journal of molecular biology · 2023Article
- Emerging Themes in CryoEM─Single Particle Analysis Image Processing.Chemical reviews · 2022Review
- Visualizing Conformational Space of Functional Biomolecular Complexes by Deep Manifold Learning.International journal of molecular sciences · 2022Article
- Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.Acta crystallographica. Section D, Structural biology · 2022Review
- Article
- Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion.Molecules (Basel, Switzerland) · 2021Article
- HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes.Frontiers in molecular biosciences · 2021Article
- Hybrid Electron Microscopy Normal Mode Analysis with Scipion.Protein science : a publication of the Protein Society · 2020Article
- Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.Acta crystallographica. Section F, Structural biology communications · 2019Review
- The first single particle analysis Map Challenge: A summary of the assessments.Journal of structural biology · 2018Article
- Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control.BioMed research international · 2016Review
- Cryo-electron Microscopy Analysis of Structurally Heterogeneous Macromolecular Complexes.Computational and structural biotechnology journal · 2016Review
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5 authors.
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Abstract
Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimensional (3D) reconstruction are usually analyzed in 3D for interpretation of structural differences. However, graphic visualization of these differences based on a quantitative analysis of elastic transformations (deformations) among density maps has not been done yet due to a lack of appropriate methods. Here, we present an approach that allows such visualization. This approach is based on statistical analysis of distances among elastically aligned pairs of EM maps (one map is deformed to fit the other map), and results in visualizing EM maps as points in a lower-dimensional distance space. The distances among points in the new space can be analyzed in terms of clusters or trajectories of points related to potential conformational changes. The results of the method are shown with synthetic and experimental EM maps at different resolutions.
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