User contributions for WikiSysop

Results for WikiSysop talk block log uploads logs
A user with 2,378 edits. Account created on 30 March 2009.
Jump to navigation Jump to search
Search for contributionsExpandCollapse
⧼contribs-top⧽
⧼contribs-date⧽
(newest | oldest) View (newer 50 | ) (20 | 50 | 100 | 250 | 500)

12 December 2025

21 November 2025

  • 11:1411:14, 21 November 2025 diff hist +1,681 N 2025Su CryoAtom Created page with "== Citation == Su, B., Huang, K., Peng, Z., Amunts, A. and Yang, J. 2025. CryoAtom improves model building for cryo-EM. Nature Structural & Molecular Biology. (2025), 1–11. == Abstract == Constructing atomic models from cryogenic electron microscopy (cryo-EM) density maps is essential for interpreting molecular mechanisms. Here we present CryoAtom, an approach for de novo model building for cryo-EM maps, leveraging recent advancements in AlphaFold2 to improve the st..." current
  • 11:1311:13, 21 November 2025 diff hist +82 Main Page →Fitting and docking
  • 11:0711:07, 21 November 2025 diff hist +1,535 N 2025Fu T2Relion Created page with "== Citation == Fu, J., Xu, J., Gan, L., Mao, T., Shen, Z., Wang, Y., Song, Z., Duan, X., Xue, W. and Yang, G. 2025. T2-RELION: Task Parallelism, Tensor Core Accelerated RELION for Cryo-EM 3D Reconstruction. Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (2025), 2186–2202. == Abstract == Cryo-electron microscopy (cryo-EM) is a key technique for structural biology, but its computational efficiency, particul..." current
  • 11:0711:07, 21 November 2025 diff hist +106 Main Page →Software

14 November 2025

  • 17:2417:24, 14 November 2025 diff hist +1,667 N 2024Shekarforoush CryoSPIN Created page with "== Citation == Shekarforoush, S., Lindell, D.B., Brubaker, M.A. and Fleet, D.J. 2024. Cryospin: improving ab-initio cryo-EM reconstruction with semi-amortized pose inference. Advances in Neural Information Processing Systems. 37, (2024), 55785–55809. == Abstract == Cryo-EM is an increasingly popular method for determining the atomic resolution 3D structure of macromolecular complexes (eg, proteins) from noisy 2D images captured by an electron microscope. The computa..." current
  • 17:2217:22, 14 November 2025 diff hist +116 Main Page →3D Alignment
  • 17:0317:03, 14 November 2025 diff hist +1,755 N 2024Wang CommonLines Created page with "== Citation == Wang, X., Jin, Q., Zou, L., Lin, X. and Lu, Y. 2024. Orientation Determination of Cryo-EM Projection Images Using Reliable Common Lines and Spherical Embeddings. IEEE/ACM Transactions on Computational Biology and Bioinformatics. (2024). == Abstract == Three-dimensional (3D) reconstruction in singleparticle cryo-electronmicroscopy (cryo-EM) is a critical technique for recovering and studying the fine 3D structure of proteins and other biological macromol..." current
  • 17:0117:01, 14 November 2025 diff hist +71 Main Page →3D Alignment

13 November 2025

  • 09:2109:21, 13 November 2025 diff hist +1,138 N 2025Chen GMM Created page with "== Citation == Chen, M. 2025. Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks. Communications Biology. 8, 1 (2025), 798. == Abstract == Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many struc..." current
  • 09:2109:21, 13 November 2025 diff hist +95 Main Page →3D Heterogeneity
  • 09:0709:07, 13 November 2025 diff hist +1,975 N 2025Selvaraj CryoTEN Created page with "== Citation == Selvaraj, J., Wang, L. and Cheng, J. 2025. CryoTEN: efficiently enhancing cryo-EM density maps using transformers. Bioinformatics. 41, 3 (2025), btaf092. == Abstract == Motivation: Cryogenic Electron Microscopy (cryo-EM) is a core experimental technique used to determine the structure of macromolecules such as proteins. However, the effectiveness of cryo-EM is often hindered by the noise and missing density values in cryo-EM density maps caused by exper..." current
  • 09:0609:06, 13 November 2025 diff hist +86 Main Page →Sharpening of high resolution information
  • 08:3708:37, 13 November 2025 diff hist +1,496 N 2025Bromberg Hand Created page with "== Citation == Bromberg, R., Guo, Y., Borek, D. and Otwinowski, Z. 2025. Validation of 3D cryoEM single-particle reconstruction correctness and handedness with Ewald’s sphere correction. Structural Dynamics. 12, 5 (2025). == Abstract == The correct description of quantum scattering places the observed scattering contributions on the Ewald's sphere and its Friedel mate copy. In electron microscopy, due to the large radius of the Ewald's sphere, these scattering contr..." current
  • 08:3608:36, 13 November 2025 diff hist +87 Main Page →Validation

12 November 2025

  • 17:3217:32, 12 November 2025 diff hist +1,671 N 2025Dhakal Benchmark Created page with "== Citation == Dhakal, A., Gyawali, R., Wang, L. and Cheng, J. 2025. Artificial intelligence in cryo-EM protein particle picking: recent advances and remaining challenges. Briefings in Bioinformatics. 26, 1 (2025), bbaf011. == Abstract == Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling the determination of high-resolution 3-Dimensional (3D) structures of large biological macromolecules. Protein particle picking, the process of iden..." current
  • 17:3117:31, 12 November 2025 diff hist +91 Main Page →Automatic particle picking
  • 16:5316:53, 12 November 2025 diff hist +1,543 N 2025Urzhumtsev RescaleFSC Created page with "== Citation == Urzhumtsev, A.G. 2025. Rescaling FSC curves. Acta Crystallographica Sec. D. 81, 11 (2025). == Abstract == Similarity between two periodic functions is commonly assessed by comparing their Fourier coefficients within resolution shells. In particular, this approach is widely used in both crystallography and cryo-electron microscopy (cryoEM). The definition of these shells, that is the choice of resolution scale for their boundaries, can be guided by the s..." current
  • 16:5316:53, 12 November 2025 diff hist +68 Main Page →Resolution
  • 16:3316:33, 12 November 2025 diff hist +1,815 N 2025Morales Membranes Created page with "== Citation == Morales-Martı́nez, A., Garduño, E., Carazo, J.M., Sorzano, C.O.S. and Vilas, J.L. 2025. Membrane and vesicle structure detection in cryo-electron tomography based on deep learning. J. Structural Biology. (2025), 108258. == Abstract == Cryo-electron tomography (cryo-ET) is a microscopy technique that enables the acquisition of 3D images of biological samples. Research in cell biology has shown that cellular processes are carried out by groups of macro..." current
  • 16:3216:32, 12 November 2025 diff hist +87 Main Page →Segmentation

6 November 2025

  • 14:0414:04, 6 November 2025 diff hist +1,367 N 2025Gusach Diffusion Created page with "== Citation == Gusach, A., Sader, K. and Russo, C.J. 2025. Outrunning protein diffusion to the air–water interface in cryoEM. Proceedings of the National Academy of Sciences. 122, 43 (2025), e2516900122. == Abstract == Here, we report a series of measurements indicating that it is physically possible to thin and vitrify a specimen for electron cryomicroscopy (cryoEM) faster than proteins diffuse to the air–water interface. We achieved this by spraying picoliter vo..." current
  • 14:0314:03, 6 November 2025 diff hist +92 Main Page →Sample preparation

5 November 2025

  • 23:3123:31, 5 November 2025 diff hist +1,530 N 2025Ni GTPick Created page with "== Citation == Ni, S., Yang, C., Liu, Y., Zhang, Y., Shi, Y., Qian, A., Kong, R. and Chang, S. 2025. GTpick: A Deep Neural Network for Cryo-EM Particle Detection. Computational and Structural Biotechnology Journal. (2025). == Abstract == Accurate identification of protein particles in cryo-electron microscopy (Cryo-EM) images is crucial for achieving high-resolution three-dimensional (3D) structural reconstruction. However, this task faces multiple challenges, includi..." current
  • 23:3023:30, 5 November 2025 diff hist +79 Main Page →Automatic particle picking

2 November 2025

  • 22:4322:43, 2 November 2025 diff hist +1,495 N 2025Elad Review Created page with "== Citation == Elad, S.T., Ben-Asher, N. and Engel, L. 2025. Cool and collected: Advances in sample preparation for cryo-electron microscopy. Current Opinion in Structural Biology. 94, (2025), 103132. == Abstract == Cryo-electron microscopy (cryo-EM) has emerged as a transformative tool in structural biology, enabling highresolution visualization of macromolecules in their native states. Cryo-focused ion beam milling (cryo-FIB) and other advances in sample preparation..." current
  • 22:4222:42, 2 November 2025 diff hist +99 Main Page →Sample preparation
  • 22:2622:26, 2 November 2025 diff hist +1,494 N 2025Muenks EmeraldID Created page with "== Citation == Muenks, A., Farrell, D.P., Zhou, G. and DiMaio, F. 2025. Automated identification of small molecules in cryoelectron microscopy data with density-and energy-guided evaluation. Structure. 33, 10 (2025), 1760–1770. == Abstract == Methodological improvements in cryoelectron microscopy (cryo-EM) have made it useful in ligandbound structure determination for biology and drug design. However, determining ligand conformation and identity is challenging at th..." current
  • 22:2622:26, 2 November 2025 diff hist +101 Main Page →Fitting and docking
  • 21:3521:35, 2 November 2025 diff hist +1,458 N 2025Li validation Created page with "== Citation == Li, D., Perez, M.M., Zhang, X., Li, J. and Jiang, W. 2025. Validation of helical symmetry parameters in EMDB. Acta Crystallographica Sec. D. 81, (2025), 527–534. == Abstract == Helical symmetry is a structural feature of many biological assemblies, including cytoskeletons, viruses and pathological amyloid fibrils. The helical parameters twist and rise are unique metadata for helical structures. With the increasing number of helical structures being re..." current
  • 21:3421:34, 2 November 2025 diff hist +93 Main Page →Validation
  • 21:2821:28, 2 November 2025 diff hist +1,395 N 2025Lauzirika Distinguishable Created page with "== Citation == Lauzirika, O., Pernica, M., Herreros, D., Ramı́rez-Aportela, E., Krieger, J., Gragera, M., Iceta, M., Conesa, P., Fonseca, Y., Jiménez, J., Flipovic, J., Carazo, J.M. and Sorzano, C.O.S. 2025. How many (distinguishable) classes can we identify in single-particle analysis? Acta Crystallographica Sec. D. 81, 10 (2025). == Abstract == Heterogeneity in cryoEM is essential for capturing the structural variability of macromolecules, reflecting their functi..." current
  • 21:1521:15, 2 November 2025 diff hist +131 Main Page →3D Heterogeneity
  • 21:1021:10, 2 November 2025 diff hist +2,335 N 2025Luo DiffFit Created page with "== Citation == Luo, D., Alsuwaykit, Z., Khan, D., Strnad, O., Isenberg, T. and Viola, I. 2025. DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map. IEEE Trans. on Visualization and Computer Graphics. 31, 1 (2025), 558–568. == Abstract == We introduce DiffFit, a differentiable algorithm for fitting protein atomistic structures into an experimental reconstructed Cryo-Electron Microscopy (cryo-EM) volume map. In structural biology, t..." current
  • 21:0521:05, 2 November 2025 diff hist +87 Main Page →Fitting and docking

16 October 2025

  • 12:4512:45, 16 October 2025 diff hist +1,732 N 2025Chen Detergent Created page with "== Citation == Chen, B., Harrison, P., Kargas, V., Pollock, N., Ford, R.C., Prince, S.M. and Collins, R.F. 2025. Coming Clean and Avoiding Bubble Trouble–Using Detergents Wisely in the Purification of Membrane Proteins for Cryo-EM Studies. Biomolecules. 15, 9 (2025), 1315. == Abstract == Detergent solubilisation remains the most commonly used but potentially problematic method to extract membrane proteins from lipid bilayers for Cryo-EM studies. Although recent adva..." current
  • 12:4512:45, 16 October 2025 diff hist +127 Main Page →Sample preparation

29 September 2025

  • 16:3116:31, 29 September 2025 diff hist +2,267 N 2025Chung CRISP Created page with "== Citation == Chung, S.-C. and Chou, P.-C. 2025. CRISP: A modular platform for cryo-EM image segmentation and processing with Conditional Random Field. J. Structural Biology. (2025), 108239. == Abstract == Distinguishing signal from background in cryogenic electron microscopy (cryo-EM) micrographs is a critical processing step but remains challenging owing to the inherently low signal-to-noise ratio (SNR), contaminants, variable ice thickness, and densely packed part..." current
  • 16:3016:30, 29 September 2025 diff hist +109 Main Page →Automatic particle picking

25 September 2025

  • 06:1406:14, 25 September 2025 diff hist +1,720 N 2020Ma RotationInvariant Created page with "== Citation == Ma, C., Bendory, T., Boumal, N., Sigworth, F. and Singer, A. 2020. Heterogeneous multireference alignment for images with application to 2D classification in single particle reconstruction. IEEE Transactions on Image Processing. 29, (2020), 1699–1710. == Abstract == Motivated by the task of 2D classification in single particle reconstruction by cryo-electron microscopy (cryo-EM), we consider the problem of heterogeneous multireference alignment of ima..." current
  • 06:1306:13, 25 September 2025 diff hist +108 Main Page →2D Classification and clustering
  • 05:5605:56, 25 September 2025 diff hist +1,810 N 2023Cesa Alignment Created page with "== Citation == Cesa, G., Pratik, K. and Behboodi, A. 2023. Equivariant self-supervised deep pose estimation for Cryo EM. Topological, Algebraic and Geometric Learning Workshops 2023 (2023), 21–36. == Abstract == Reconstructing the 3D volume of a molecule from its differently oriented 2D projections is the central problem of Cryogenic Electron Microscopy (cryo-EM), one of the main techniques for macro-molecule imaging. Because the orientations are unknown, the estima..." current
  • 05:5505:55, 25 September 2025 diff hist +113 Main Page →3D Alignment

22 September 2025

  • 16:2316:23, 22 September 2025 diff hist +1,915 N 2025Matsuoka ForceConstant Created page with "== Citation == Matsuoka, D., Sugita, Y. and Mori, T. 2025. An Empirical Biasing Force Constant to Minimize Overfitting in Cryo-EM Flexible Fitting Refinement. J. Chemical Information and Modelling. (2025). == Abstract == Reliable modeling of protein structures from a cryo- EM density map is one of the central issues in structural biology. Typically, the constructed model is refined using a flexible fitting method combined with molecular dynamics, where a biasing poten..." current
  • 16:2216:22, 22 September 2025 diff hist +115 Main Page →Fitting and docking

17 September 2025

11 September 2025

  • 07:4707:47, 11 September 2025 diff hist +1,792 N 2025Khoshbin Magellon Created page with "== Citation == Khoshbin, B., Damodar, P., Garje, R.R., Schotanus, F.H., Nair, N., Wei, L., Schaefer, J.-H., Lander, G.C., Cianfrocco, M.A. and Stagg, S.M. 2025. Magellon-an extensible platform for cryo-EM data visualization, management, and processing. IUCrJ. 12, (2025), eh5023. == Abstract == Single-particle cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling high-resolution determination of macromolecular structures. However, the fie..." current
  • 07:4507:45, 11 September 2025 diff hist +101 Main Page →Software
  • 07:3507:35, 11 September 2025 diff hist +1,488 N 2025 Huang Created page with "== Citation == Huang, M., Ma, J., Fu, X., Wang, H., Shen, Y. and Li, X. 2025. Accurate helical parameter estimation based on cylindrical unrolling. Structure. (2025). == Abstract == Helical structure is fundamental for filamentous and tubular macromolecular assemblies that play crucial roles in structural scaffolding and signaling processes. Structure determination of these assemblies relies on the precise estimation of their helical parameters. Although layer-line-ba..." current
(newest | oldest) View (newer 50 | ) (20 | 50 | 100 | 250 | 500)
Retrieved from "https://3demmethods.i2pc.es/index.php/Special:Contributions/WikiSysop"