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A user with 2,378 edits. Account created on 30 March 2009.
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3 January 2025

  • 08:0208:02, 3 January 2025 diff hist +1,465 N 2023Lucas Baited Created page with "== Citation == B. A. Lucas, B. A. Himes, and N. Grigorieff, “Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias,” Elife, vol. 12, p. RP90486, 2023. == Abstract == Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and c..." current
  • 08:0208:02, 3 January 2025 diff hist +86 Main Page →Automatic particle picking
  • 07:5507:55, 3 January 2025 diff hist +1,442 N 2024Bhattacharjee TimeResolved Created page with "== Citation == S. Bhattacharjee et al., “Time resolution in cryo-EM using a PDMS-based microfluidic chip assembly and its application to the study of HflX-mediated ribosome recycling,” Cell, vol. 187, no. 3, pp. 782–796, 2024. == Abstract == The rapid kinetics of biological processes and associated short-lived conformational changes pose a significant challenge in attempts to structurally visualize biomolecules during a reaction in real time. Conventionally, on-..." current
  • 07:5407:54, 3 January 2025 diff hist +99 Main Page →Sample preparation
  • 07:5007:50, 3 January 2025 diff hist +1,416 N 2024Tuijtel Lamellae Created page with "== Citation == M. W. Tuijtel et al., “Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging,” Science Advances, vol. 10, no. 17, p. eadk6285, 2024. == Abstract == Cryo–electron tomography (cryo-ET) is a powerful method to elucidate subcellular architecture and to structurally analyze biomolecules in situ by subtomogram averaging, yet data quality critically depends on specimen thickness. Cells that are too thick for transmission imagin..." current
  • 07:4907:49, 3 January 2025 diff hist +87 Main Page →Sample preparation
  • 07:4507:45, 3 January 2025 diff hist +1,890 N 2023Grassetti Graphene Created page with "== Citation == A. V. Grassetti, M. B. May, and J. H. Davis, “Enhancing CryoEM Sample Preparation Using Graphene Monolayer on Microscopy Grids (Video)| JoVE,” JoVE (Journal of Visualized Experiments), no. 201, p. e66023, 2023. == Abstract == In cryogenic electron microscopy (cryoEM), purified macromolecules are applied to a grid bearing a holey carbon foil; the molecules are then blotted to remove excess liquid and rapidly frozen in a roughly 20-100 nm thick layer..." current
  • 07:4407:44, 3 January 2025 diff hist +91 Main Page →Sample preparation

27 December 2024

  • 07:5807:58, 27 December 2024 diff hist +1,497 N 2023DiIorio AbInitio Created page with "== Citation == M. C. DiIorio and A. W. Kulczyk, “Novel artificial intelligence-based approaches for ab initio structure determination and atomic model building for cryo-electron microscopy,” Micromachines, vol. 14, no. 9, p. 1674, 2023. == Abstract == Single particle cryo-electron microscopy (cryo-EM) has emerged as the prevailing method for near-atomic structure determination, shedding light on the important molecular mechanisms of biological macromolecules. Howe..." current
  • 07:5707:57, 27 December 2024 diff hist +110 Main Page →Books and reviews
  • 07:5307:53, 27 December 2024 diff hist +1,473 N 2023Langeberg RNAScaffold Created page with "== Citation == C. J. Langeberg and J. S. Kieft, “A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM,” Nucleic Acids Research, vol. 51, no. 20, pp. e100–e100, 2023. == Abstract == Single-particle cryo-electron microscopy (cryo-EM) can reveal the structures of large and often dynamic molecules, but smaller biomolecules remain challenging targets due to their intrinsic low signal to noise ratio. Methods to resolve small proteins..." current
  • 07:5207:52, 27 December 2024 diff hist +79 Main Page →Sample preparation
  • 07:3707:37, 27 December 2024 diff hist +1,596 N 2023Riahi Transport Created page with "== Citation == A. T. Riahi, G. Woollard, F. Poitevin, A. Condon, and K. D. Duc, “Alignot: An optimal transport based algorithm for fast 3d alignment with applications to cryogenic electron microscopy density maps,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023. == Abstract == Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step re..." current
  • 07:3607:36, 27 December 2024 diff hist +95 Main Page →3D Alignment
  • 07:1907:19, 27 December 2024 diff hist +1,068 N 2024Singer Wasserstein Created page with "== Citation == A. Singer and R. Yang, “Alignment of density maps in Wasserstein distance,” Biological Imaging, vol. 4, p. e5, 2024. == Abstract == In this article, we propose an algorithm for aligning three-dimensional objects when represented as density maps, motivated by applications in cryogenic electron microscopy. The algorithm is based on minimizing the 1-Wasserstein distance between the density maps after a rigid transformation. The induced loss function en..." current
  • 07:1807:18, 27 December 2024 diff hist +98 Main Page →3D Alignment

26 December 2024

  • 11:0111:01, 26 December 2024 diff hist +1,531 N 2023Forsberg Filter Created page with "== Citation == B. O. Forsberg, P. N. Shah, and A. Burt, “A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps,” Nature Communications, vol. 14, no. 1, p. 5802, 2023. == Abstract == Cryo electron microscopy (cryo-EM) is used by biological research to visualize biomolecular complexes in 3D, but the heterogeneity of cryo-EM reconstructions is not easily estimated. Current processing paradigms nevertheless exert great eff..." current
  • 11:0111:01, 26 December 2024 diff hist +84 Main Page →3D Heterogeneity
  • 10:5010:50, 26 December 2024 diff hist +1,428 N 2023Dai CryoFEM Created page with "== Citation == X. Dai, L. Wu, S. Yoo, and Q. Liu, “Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps,” Briefings in Bioinformatics, vol. 24, no. 6, p. bbad405, 2023. == Abstract == Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3-D atomic models of biological molecules. AlphaFold-predicted models generate initial 3-D coordinates; however, model inaccuracy and conformational heterogeneity o..." current
  • 10:4910:49, 26 December 2024 diff hist +103 Main Page →Fitting and docking
  • 10:4410:44, 26 December 2024 diff hist +1,621 N 2023Afonine Varref Created page with "== Citation == P. V. Afonine, A. Gobet, L. Moissonnier, J. Martin, B. K. Poon, and V. Chaptal, “Conformational space exploration of cryo-EM structures by variability refinement,” Biochimica et Biophysica Acta (BBA)-Biomembranes, vol. 1865, no. 4, p. 184133, 2023. == Abstract == Cryo-EM observation of biological samples enables visualization of sample heterogeneity, in the form of discrete states that are separable, or continuous heterogeneity as a result of local..." current
  • 10:4410:44, 26 December 2024 diff hist +98 Main Page →3D Heterogeneity
  • 10:4010:40, 26 December 2024 diff hist +2,095 N 2023Yee Ot2Rec Created page with "== Citation == N. B.-y. Yee, E. M. Ho, M. Darrow, and M. Basham, “Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow,” Biophysical Journal, vol. 122, no. 3, p. 462a, 2023. == Abstract == Electron cryo-tomography is an imaging technique for probing 3D structures with at the nanometer scale. This technique has been used extensively in the biomedical field to study the complex structures of proteins and other macromolecules. With..." current
  • 10:3810:38, 26 December 2024 diff hist +75 Main Page →Software

23 December 2024

  • 20:1320:13, 23 December 2024 diff hist +2,019 N 2023Zhang Denoising Created page with "== Citation == D. Zhang et al., “Unsupervised Cryo-EM Images Denoising and Clustering based on Deep Convolutional Autoencoder and K-Means++,” IEEE Trans. Medical Imaging, vol. 42, pp. 1509–1521, 2023. == Abstract == Cryo-electron microscopy (cryo-EM) is a widely used structural determination technique. Because of the extremely low signal-to-noise ratio (SNR) of images captured by cryo-EM, clustering single-particle cryo-EM images with high accuracy is challengin..." current
  • 20:0820:08, 23 December 2024 diff hist +118 Main Page →2D Preprocessing
  • 20:0420:04, 23 December 2024 diff hist −5 2024Bendory Complexity No edit summary current
  • 20:0320:03, 23 December 2024 diff hist +1,962 N 2024Bendory Complexity Created page with "== Citation == T. Bendory and D. Edidin, “The Sample Complexity of Sparse Multireference Alignment and Single-Particle Cryo-Electron Microscopy,” SIAM J. on Mathematics of Data Science, vol. 6, no. 2, pp. 254–282, 2024. == Abstract == Multireference alignment (MRA) is the problem of recovering a signal from its multiple noisy copies, each acted upon by a random group element. MRA is mainly motivated by single-particle cryo–electron microscopy (cryo-EM) that ha..."
  • 20:0320:03, 23 December 2024 diff hist +103 Main Page →2D Alignment
  • 19:5819:58, 23 December 2024 diff hist +1,551 N 2024Liu DeepETPicker Created page with "== Citation == G. Liu, T. Niu, M. Qiu, Y. Zhu, F. Sun, and G. Yang, “DeepETPicker: Fast and accurate 3D particle picking for cryo-electron tomography using weakly supervised deep learning,” Nature Communications, vol. 15, no. 1, p. 2090, 2024. == Abstract == To solve three-dimensional structures of biological macromolecules in situ, large numbers of particles often need to be picked from cryo-electron tomograms. However, adoption of automated particle-picking meth..." current
  • 19:5819:58, 23 December 2024 diff hist +94 Main Page →Subtomogram analysis
  • 19:5419:54, 23 December 2024 diff hist +1,478 N 2023Rice TomoTwin Created page with "== Citation == G. Rice, T. Wagner, M. Stabrin, O. Sitsel, D. Prumbaum, and S. Raunser, “TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining,” Nature methods, vol. 20, no. 6, pp. 871–880, 2023. == Abstract == Cryogenic-electron tomography enables the visualization of cellular environments in extreme detail, however, tools to analyze the full amount of information contained within these densely packed volu..." current
  • 19:5319:53, 23 December 2024 diff hist +71 Main Page →Subtomogram analysis
  • 19:5019:50, 23 December 2024 diff hist +1,403 N 2023Weiss Noise Created page with "== Citation == G. Weiss-Dicker, A. Eldar, Y. Shkolinsky, and T. Bendory, “Unsupervised particle sorting for cryo-EM using probabilistic PCA,” in 2023 IEEE 20th Intl. Symposium on Biomedical Imaging (ISBI), IEEE, 2023, pp. 1–5. == Abstract == Single-particle cryo-electron microscopy (cryo-EM) is a leading technology to resolve the structure of molecules. Early in the process, the user detects potential particle images in the raw data. Typically, there are many fa..." current
  • 19:5019:50, 23 December 2024 diff hist +91 Main Page →2D Classification and clustering
  • 19:4319:43, 23 December 2024 diff hist +1,330 N 2024Jamali Modelangelo Created page with "== Citation == K. Jamali, L. Käll, R. Zhang, A. Brown, D. Kimanius, and S. H. Scheres, “Automated model building and protein identification in cryo-EM maps,” Nature, vol. 628, no. 8007, pp. 450–457, 2024. == Abstract == Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention in three-dimensional computer graphics programs1,2. Here we present ModelAngelo, a machine-learnin..." current
  • 19:4219:42, 23 December 2024 diff hist +96 Main Page →Fitting and docking
  • 19:3419:34, 23 December 2024 diff hist +1,665 N 2023Beton Fitting Created page with "== Citation == J. G. Beton, T. Cragnolini, M. Kaleel, T. Mulvaney, A. Sweeney, and M. Topf, “Integrating model simulation tools and cryo-electron microscopy,” Wiley Interdisciplinary Reviews: Computational Molecular Science, vol. 13, no. 3, p. e1642, 2023. == Abstract == The power of computer simulations, including machine-learning, has become an inseparable part of scientific analysis of biological data. This has significantly impacted the field of cryogenic elec..." current
  • 19:3319:33, 23 December 2024 diff hist 0 Main Page →Books and reviews
  • 19:3219:32, 23 December 2024 diff hist +72 Main Page →Books and reviews
  • 19:2719:27, 23 December 2024 diff hist +1,040 N 2023Geva AbInitio Created page with "== Citation == A. S. Geva and Y. Shkolnisky, “A common lines approach for ab initio modeling of molecules with tetrahedral and octahedral symmetry,” SIAM J. on Imaging Sciences, vol. 16, no. 4, pp. 1978–2014, 2023. == Abstract == A main task in cryo-electron microscopy single particle reconstruction is to nd a three-dimensional model of a molecule given a set of its randomly oriented and positioned noisy projection-images. In this work, we propose an algorithm f..." current
  • 19:2619:26, 23 December 2024 diff hist +114 Main Page →3D Reconstruction

19 December 2024

  • 08:1608:16, 19 December 2024 diff hist +1,166 N 2023Harpaz Alignment Created page with "== Citation == Y. Harpaz and Y. Shkolnisky, “Three-dimensional alignment of density maps in cryo-electron microscopy,” Biological Imaging, vol. 3, p. e8, 2023. == Abstract == A common task in cryo-electron microscopy data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for aligning three-dimensional density maps, which exploits common lines between projection images of the maps. The algorithm is ful..." current
  • 08:1308:13, 19 December 2024 diff hist +88 Main Page →3D Alignment
  • 08:0208:02, 19 December 2024 diff hist +1,747 N 2022Bharadwaj Scattering Created page with "== Citation == A. Bharadwaj and A. J. Jakobi, “Electron scattering properties of biological macromolecules and their use for cryo-EM map sharpening,” Faraday Discussions, vol. 240, pp. 168–183, 2022. == Abstract == Resolution-dependent loss of contrast in cryo-EM maps may obscure features at high resolution that are critical for map interpretation. Post-processing of cryo-EM maps can improve the interpretability by adjusting the resolution-dependence of structur..." current
  • 08:0108:01, 19 December 2024 diff hist +110 Main Page →Image formation

12 December 2024

  • 08:4008:40, 12 December 2024 diff hist +1,635 N 2024Karimi Vesicle Created page with "== Citation == R. Karimi, C. E. Coupland, and J. L. Rubinstein, “Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles,” J. Structural Biology, vol. 216, no. 4, p. 108148, 2024. == Abstract == Electron cryomicroscopy (cryo-EM) has recently allowed determination of near-atomic resolution structures of membrane proteins and protein complexes embedded in lipid vesicles. However, particle selection from electron micrographs of t..." current
  • 08:3908:39, 12 December 2024 diff hist +81 Main Page →Subtomogram analysis
  • 08:3508:35, 12 December 2024 diff hist +1,978 N 2024Remis Damage Created page with "== Citation == J. Remis et al., “Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage,” Journal of Structural Biology, p. 108150, 2024. == Abstract == Apoferritin (apoF) is commonly used as a test specimen in single-particle electron cryo-microscopy (cryo-EM), since it consistently produces density maps that go to 3 Å resolution or higher. When we imaged apoF with a laser phase plate (LPP), however, we observed more severe particle-to-p..." current
  • 08:3508:35, 12 December 2024 diff hist +80 Main Page →Image formation
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