User contributions for WikiSysop

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A user with 2,400 edits. Account created on 30 March 2009.
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23 December 2024

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
  • 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
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