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A user with 2,122 edits. Account created on 30 March 2009.
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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 current

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
  • 06:5506:55, 6 September 2024 diff hist +92‎ Main Page ‎ →‎3D Alignment
  • 06:4906:49, 6 September 2024 diff hist +2,167‎ N 2023Rangan Fast ‎ Created page with "== Citation == Rangan, Aaditya V. Radial recombination for rigid rotational alignment of images and volumes. 2023. Inverse Problems, Vol. 39, No. 1, p. 015003 == Abstract == A common task in single particle electron cryomicroscopy (cryo-EM) is the rigid alignment of images and/or volumes. In the context of images, a rigid alignment involves estimating the inner product between one image of N × N pixels and another image that has been translated by some displaceme..." current
  • 06:4806:48, 6 September 2024 diff hist +82‎ Main Page ‎ →‎3D Alignment
  • 06:3806:38, 6 September 2024 diff hist +1,960‎ N 2022Ganguly SparseAlign ‎ Created page with "== Citation == Ganguly, Poulami Somanya / Lucka, Felix / Kohr, Holger / Franken, Erik / Hupkes, Hermen Jan / Batenburg, Kees Joost. Sparsealign: A grid-free algorithm for automatic marker localization and deformation estimation in cryo-electron tomography. 2022. IEEE Transactions on Computational Imaging, Vol. 8, p. 651-665 == Abstract == Tilt-series alignment is crucial to obtaining high-resolution reconstructions in cryo-electron tomography. Beam-induced local defor..." current
  • 06:3706:37, 6 September 2024 diff hist +117‎ Main Page ‎ →‎Image alignment
  • 06:3206:32, 6 September 2024 diff hist +1,535‎ N 2022Terwilliger AlphaFold ‎ Created page with "== Citation == Terwilliger, Thomas C. / Poon, Billy K. / Afonine, Pavel V. / Schlicksup, Christopher J. / Croll, Tristan I. / Millán, Claudia / Richardson, Jane S. / Read, Randy J. / Adams, Paul D. Improved AlphaFold modeling with implicit experimental information. 2022. Nature methods, Vol. 19, No. 11, p. 1376-1382 == Abstract == Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models u..." current
  • 06:3106:31, 6 September 2024 diff hist +104‎ Main Page ‎ →‎Fitting and docking

5 September 2024

  • 06:4106:41, 5 September 2024 diff hist +1,439‎ N 2022Arnold liganded ‎ Created page with "== Citation == Arnold, William R. / Asarnow, Daniel / Cheng, Yifan. Classifying liganded states in heterogeneous single-particle cryo-EM datasets. 2022. Microscopy, Vol. 71, No. Supplement_1, p. i23-i29 == Abstract == A powerful aspect of single-particle cryogenic electron microscopy is its ability to determine high-resolution structures from samples containing heterogeneous mixtures of the same macromolecule in different conformational or compositional states. Beyond..." current
  • 06:4006:40, 5 September 2024 diff hist +88‎ Main Page ‎ →‎3D Heterogeneity
  • 06:3306:33, 5 September 2024 diff hist +1,740‎ N 2021Moebel DeepFinder ‎ Created page with "== Citation == Moebel, Emmanuel / Martinez-Sanchez, Antonio / Lamm, Lorenz / Righetto, Ricardo D. / Wietrzynski, Wojciech / Albert, Sahradha / Larivière, Damien / Fourmentin, Eric / Pfeffer, Stefan / Ortiz, Julio / others. Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms. 2021. Nature methods, Vol. 18, No. 11, p. 1386-1394 Abstract: Cryogenic electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecule..." current
  • 06:3206:32, 5 September 2024 diff hist +117‎ Main Page ‎ →‎Subtomogram analysis

4 September 2024

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