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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 current
- 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
- 08:3008:30, 12 December 2024 diff hist +1,677 N 2024Hsieh MinIce Created page with "== Citation == C.-C. Hsieh, Z.-J. Lin, and L.-J. Lai, “Minimizing ice contamination during specimen preparation for cryo-soft X-ray tomography and cryo-electron tomography,” Journal of Structural Biology: X, vol. 10, p. 100113, 2024. == Abstract == Cryo-soft X-ray tomography (cryo-SXT) is a newly developed technique for imaging 3D whole cells in nearly native states. Cryo-SXT users require the preparation of numerous cryo-sample grids to use the allocated beamtime..." current
- 08:2908:29, 12 December 2024 diff hist +86 Main Page →Sample preparation
- 08:0408:04, 12 December 2024 diff hist +1,504 N 2024Schiotz Review Created page with "== Citation == O. H. Schiøtz, S. Klumpe, J. M. Plitzko, and C. J. Kaiser, “Cryo-electron tomography: en route to the molecular anatomy of organisms and tissues,” Biochemical Society Transactions, p. BST20240173, 2024. == Abstract == Cryo-electron tomography (cryo-ET) has become a key technique for obtaining structures of macromolecular complexes in their native environment, assessing their local organization and describing the molecular sociology of the cell. Whi..." current
- 08:0408:04, 12 December 2024 diff hist +78 Main Page →Books and reviews
- 06:3406:34, 12 December 2024 diff hist +1,408 N 2024Harley 40 Created page with "== Citation == I. Harley, F. Mazzotta, X. Shaulli, F. Scheffold, K. Landfester, and I. Lieberwirth, “Practical considerations for plunge freezing samples over 40° C for Cryo-EM,” Micron, p. 103745, 2024. == Abstract == Cryo-EM is now an established tool for examining samples in their native, hydrated states—a leap made possible by vitrification. Utilising this sample preparation method to directly visualise temperature-responsive samples allows for deeper insig..." current
- 06:3306:33, 12 December 2024 diff hist +65 Main Page →Sample preparation
18 November 2024
- 15:0715:07, 18 November 2024 diff hist +1,770 N 2024deLaRosa EMHub Created page with "== Citation == J. M. de la Rosa-Trevin et al., “EMhub: a web platform for data management and on-the-fly processing in scientific facilities,” Biological Crystallography, vol. 80, no. 11, 2024. == Abstract == Most scientific facilities produce large amounts of heterogeneous data at a rapid pace. Managing users, instruments, reports and invoices presents additional challenges. To address these challenges, EMhub, a web platform designed to support the daily operatio..." current
- 15:0615:06, 18 November 2024 diff hist +113 Main Page →Software
8 November 2024
- 10:3110:31, 8 November 2024 diff hist +1,532 N 2024Cameron REPIC Created page with "== Citation == C. J. Cameron, S. J. Seager, F. J. Sigworth, H. D. Tagare, and M. B. Gerstein, “REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers,” Communications Biology, vol. 7, no. 1, p. 1421, 2024. == Abstract == Cryo-EM particle identification from micrographs (“picking”) is challenging due to the low signal-to-noise ratio and lack of ground truth for particle locations. State-of-the-art computa..." current
- 10:3110:31, 8 November 2024 diff hist +82 Main Page →Automatic particle picking
- 10:2810:28, 8 November 2024 diff hist +1,474 N 2024Li EM2NA Created page with "== Citation == T. Li, H. Cao, J. He, and S.-Y. Huang, “Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps,” Nature Communications, vol. 15, no. 1, p. 9367, 2024. == Abstract == Cryo-electron microscopy (cryo-EM) is one of the most powerful experimental methods for macromolecular structure determination. However, accurate DNA/RNA structure modeling from cryo-EM maps is still challenging especially for protein-DNA/RNA or multi-chai..." current
- 10:2710:27, 8 November 2024 diff hist +105 Main Page →Fitting and docking
- 10:2210:22, 8 November 2024 diff hist +494 N 2024Ermel DataPortal Created page with "== Citation == U. Ermel et al., “A data portal for providing standardized annotations for cryo-electron tomography,” Nature Methods, pp. 1–3, 2024. == Abstract == We present the cryoET Data Portal (https://cryoetdataportal. czscience.com/), containing annotated cryoET datasets in standardized formats, as a resource for the cryoET community == Keywords == == Links == https://www.nature.com/articles/s41592-024-02477-2 == Related software == == Related methods..." current
- 10:2110:21, 8 November 2024 diff hist +61 Main Page →Databases
- 10:1610:16, 8 November 2024 diff hist +1,220 N 2024Wang DiffModeller Created page with "== Citation == X. Wang, H. Zhu, G. Terashi, M. Taluja, and D. Kihara, “DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model,” Nature Methods, pp. 1–11, 2024. == Abstract == Cryogenic electron microscopy (cryo-EM) has now been widely used for determining multichain protein complexes. However, modeling a large complex structure, such as those with more than ten chains, is challenging, particularly when the map resolution de..." current
- 10:1510:15, 8 November 2024 diff hist +110 Main Page →Fitting and docking
- 10:1110:11, 8 November 2024 diff hist +1,113 N 2024Anuk Auction Created page with "== Citation == S. Anuk, T. Bendory, and A. Painsky, “Image detection using combinatorial auction,” IEEE Open J. Signal Processing, 2024. == Abstract == This paper studies the optimal solution of the classical problem of detecting the location of multiple image occurrences in a two-dimensional, noisy measurement. Assuming the image occurrences do not overlap, we formulate this task as a constrained maximum likelihood optimization problem.We show that the maximum li..." current
- 10:1010:10, 8 November 2024 diff hist +83 Main Page →Automatic particle picking
- 10:0610:06, 8 November 2024 diff hist +1,856 N 2024Chen EModelX Created page with "== Citation == S. Chen, S. Zhang, X. Fang, L. Lin, H. Zhao, and Y. Yang, “Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences,” Nature Communications, vol. 15, no. 1, p. 8808, 2024. == Abstract == Cryo-electron microscopy (cryo-EM) technique is widely used for protein structure determination. Current automatic cryo-EM protein complex modeling methods mostly rely on prior chain separation. However, chain separation..." current
- 10:0410:04, 8 November 2024 diff hist +80 Main Page →Fitting and docking
- 10:0010:00, 8 November 2024 diff hist +1,468 N 2024Moriya GoToCloud Created page with "== Citation == T. Moriya, Y. Yamada, M. Yamamoto, and T. Senda, “GoToCloud optimization of cloud computing environment for accelerating cryo-EM structure-based drug design,” Communications Biology, vol. 7, no. 1, p. 1320, 2024. == Abstract == Cryogenic electron microscopy (Cryo-EM) is a widely used technique for visualizing the 3D structures of many drug design targets, including membrane proteins, at atomic resolution. However, the necessary throughput for struct..." current
- 09:5909:59, 8 November 2024 diff hist +81 Main Page →Software
- 09:4609:46, 8 November 2024 diff hist +1,875 N 2024Joosten Roodmus Created page with "== Citation == M. Joosten, J. Greer, J. Parkhurst, T. Burnley, and A. J. Jakobi, “Roodmus: A toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions,” IUCrJ, vol. 11, no. 6, 2024. == Abstract == Conformational heterogeneity of biological macromolecules is a challenge in single-particle averaging (SPA). Current standard practice is to employ classification and filtering methods that may allow a discrete number of conformational states to be..." current
- 09:4509:45, 8 November 2024 diff hist +100 Main Page →Image formation
- 09:3709:37, 8 November 2024 diff hist +1,482 N 2024Li Subtraction Created page with "== Citation == S. Li, M. Li, Y. Wang, and X. Li, “Subtraction of liposome signals in cryo-EM structural determination of protein-liposome complexes,” Chinese Physics B, 2024. == Abstract == Reconstituting membrane proteins in liposomes and determining their structure is a common method for determining membrane protein structures using single-particle cryo-electron microscopy (cryo-EM). However, the strong signal of liposomes under cryo-EM imaging conditions often..." current
- 09:3409:34, 8 November 2024 diff hist +78 Main Page →2D Preprocessing
22 October 2024
- 14:4814:48, 22 October 2024 diff hist +1,209 N 2024Lander Validation Created page with "== Citation == G. C. Lander, “Single particle cryo-EM map and model validation: It’s not crystal clear,” Current Opinion in Structural Biology, vol. 89, p. 102918, 2024. == Abstract == The application of single particle cryogenic electron microscopy (cryo-EM) to structure determination continues to have a transformative impact on our understanding on biological systems. While there has been a great deal of algorithmic development focused on improving attainable..." current
- 14:4814:48, 22 October 2024 diff hist +67 Main Page →Books and reviews
18 October 2024
- 06:5206:52, 18 October 2024 diff hist +2,232 N 2023Sazzed Struwwel Created page with "== Citation == S. Sazzed, P. Scheible, J. He, and W. Wriggers, “Untangling irregular actin cytoskeleton architectures in tomograms of the cell with struwwel tracer,” Intl. J. Molecular Sciences, vol. 24, no. 24, p. 17183, 2023. == Abstract == In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellu..." current
- 06:5106:51, 18 October 2024 diff hist +85 Main Page →Segmentation
- 06:4006:40, 18 October 2024 diff hist +1,459 N 2024Sanchez Anisotropy Created page with "== Citation == R. Sanchez-Garcia, G. Gaullier, J. M. Cuadra-Troncoso, and J. Vargas, “Cryo-EM map anisotropy can be attenuated by map post-processing and a new method for its estimation,” Intl. J. Molecular Sciences, vol. 25, no. 7, p. 3959, 2024. == Abstract == One of the most important challenges in cryogenic electron microscopy (cryo-EM) is the substantial number of samples that exhibit preferred orientations, which leads to an uneven coverage of the projection..." current
- 06:3906:39, 18 October 2024 diff hist +78 Main Page →Validation
- 05:5505:55, 18 October 2024 diff hist +1,644 N 2024vanVeen Missing Created page with "== Citation == D. Van Veen et al., “Missing wedge completion via unsupervised learning with coordinate networks,” Intl. J. Molecular Sciences, vol. 25, no. 10, p. 5473, 2024. == Abstract == Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction qua..." current
- 05:5405:54, 18 October 2024 diff hist +71 Main Page →3D reconstruction
- 05:3105:31, 18 October 2024 diff hist +1,784 N 2023Ling Synch Created page with "== Citation == S. Ling, “Solving orthogonal group synchronization via convex and low-rank optimization: Tightness and landscape analysis,” Mathematical Programming, vol. 200, no. 1, pp. 589–628, 2023. == Abstract == Group synchronization aims to recover the group elements from their noisy pairwise measurements. It has found many applications in community detection, clock synchronization, and joint alignment problem. This paper focuses on the orthogonal group syn..." current
- 05:3105:31, 18 October 2024 diff hist 0 Main Page →3D Alignment
- 05:3005:30, 18 October 2024 diff hist +77 Main Page →3D Alignment
8 October 2024
- 10:5410:54, 8 October 2024 diff hist +1,605 N 2024Huang MiLoPYP Created page with "== Citation == Q. Huang, Y. Zhou, and A. Bartesaghi, “MiLoPYP: self-supervised molecular pattern mining and particle localization in situ,” Nature Methods, pp. 1–10, 2024. == Abstract == Cryo-electron tomography allows the routine visualization of cellular landscapes in three dimensions at nanometer-range resolutions. When combined with single-particle tomography, it is possible to obtain near-atomic resolution structures of frequently occurring macromolecules w..." current
- 10:5310:53, 8 October 2024 diff hist +89 Main Page →Subtomogram analysis
7 October 2024
- 17:0317:03, 7 October 2024 diff hist +1,456 N 2024Abe LEA Created page with "== Citation == K. M. Abe, G. Li, Q. He, T. Grant, and C. J. Lim, “Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing,” Nature Communications, vol. 15, no. 1, p. 7705, 2024. == Abstract == Air-water interface (AWI) interactions during cryo-electron microscopy (cryo-EM) sample preparation cause significant sample loss, hindering structural biology research. Organisms like nematodes and tardigrades produce Late Em..." current
- 17:0317:03, 7 October 2024 diff hist +91 Main Page →Sample preparation
6 September 2024
- 06:5606:56, 6 September 2024 diff hist +1,904 N 2022Levy CryoAI Created page with "== Citation == Levy, Axel / Poitevin, Frédéric / Martel, Julien / Nashed, Youssef / Peck, Ariana / Miolane, Nina / Ratner, Daniel / Dunne, Mike / Wetzstein, Gordon. Cryoai: Amortized inference of poses for ab initio reconstruction of 3d molecular volumes from real cryo-em images. 2022. European Conference on Computer Vision, p. 540-557 == Abstract == Cryo-electron microscopy (cryo-EM) has become a tool of fundamental importance in structural biology, helping us unde..." current