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A user with 2,396 edits. Account created on 30 March 2009.
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7 January 2026

  • 08:1408:14, 7 January 2026 diff hist +1,873 N 2026Mulvaney CASP16 Created page with "== Citation == Mulvaney, T., Kryshtafovych, A. and Topf, M. 2026. Cryo-EM Analysis in CASP16. Proteins: Structure, Function, and Bioinformatics. (2026). == Abstract == Since CASP13, experimentalists have been encouraged to provide their cryo-EM data along with the derived atomic models to the CASP organizers to aid assessment. In CASP16, 38 cryo-EM datasets were provided for assessment, which represented most cryo-EM targets. The corresponding targets typically compri..." current
  • 08:1308:13, 7 January 2026 diff hist +123 Main Page →Fitting and docking current
  • 08:0608:06, 7 January 2026 diff hist +1,145 N 2025Tang CryoLike Created page with "== Citation == Tang, W.S., Soules, J., Rangan, A. and Cossio, P. 2025. CryoLike: a Python package for cryo-electron microscopy image-to-structure likelihood calculations. Biological Crystallography. 81, 12 (2025). == Abstract == Extracting conformational heterogeneity from cryo-electron microscopy (cryo-EM) images is particularly challenging for flexible biomolecules, where traditional 3D classification approaches often fail. Over the past few decades, advancements in..." current
  • 08:0508:05, 7 January 2026 diff hist +86 Main Page →2D Alignment

30 December 2025

  • 09:2509:25, 30 December 2025 diff hist +1,381 N 2025Li EMProt Created page with "== Citation == Li, T., Chen, J., Li, H., Cao, H. and Huang, S.-Y. 2025. EMProt improves structure determination from cryo-EM maps. Nature Structural & Molecular Biology. (2025), 1–10. == Abstract == Cryo-electron microscopy (cryo-EM) has become the mainstream technique for macromolecular structure determination. However, because of intrinsic resolution heterogeneity, accurate modeling of all-atom structure from cryo-EM maps remains challenging even for maps at near-..." current
  • 09:2409:24, 30 December 2025 diff hist +95 Main Page →Fitting and docking
  • 08:4808:48, 30 December 2025 diff hist +1,320 N 2025Leone Review Created page with "== Citation == Leone, V. and Marinelli, F. 2025. From snapshots to ensembles: Integrating experimental data and dynamics. Current Opinion in Structural Biology. 95, (2025), 103155. == Abstract == Protein function arises from the interplay of structure, dynamics, and biomolecular interactions. Despite advances in cryo-EM and AI-based structure prediction, capturing dynamic and energetic features remains a challenge. Biophysical methods like NMR, EPR, HDX-MS, SAXS, and..." current
  • 08:4708:47, 30 December 2025 diff hist +114 Main Page →Books and reviews

29 December 2025

  • 09:2909:29, 29 December 2025 diff hist +1,871 N 2025Peng DiamTR Created page with "== Citation == Peng, R., Elkhaligy, H., Grant, T. and Stagg, S.M. 2025. DiameTR: A cryo-EM tool for diameter sorting of tubular samples. J. Structural Biology: X. (2025), 100136. == Abstract == Tubular structures are ubiquitous in biological systems and have been a focal point of cryo-electron microscopy (cryo-EM) structural analysis since the technique’s inception. A critical step in processing tubular cryo-EM data is particle classification by diameter, as uniform..." current
  • 09:2909:29, 29 December 2025 diff hist +85 Main Page →Filament picking
  • 09:0209:02, 29 December 2025 diff hist +1,474 N 2025Chen CryoEvoBuilding Created page with "== Citation == Chen, J., Li, T., He, J. and Huang, S.-Y. 2025. Protein model building for intermediate-resolution cryo-EM maps by integrating evolutionary and experimental information. Structure. (2025). == Abstract == Accurate model building in intermediate-resolution cryo-EM maps normally requires flexible fitting of reliable initial structures. However, while deep learning-based methods such as AlphaFold2 can predict highly accurate structures, the predicted struct..." current
  • 09:0209:02, 29 December 2025 diff hist +142 Main Page →Fitting and docking
  • 08:5008:50, 29 December 2025 diff hist +1,938 N 2025Chen Asymmetric Created page with "== Citation == Chen, W., Zheng, J., Zhou, J., Cheng, L. and Liu, H. 2025. A data-processing strategy of asymmetric reconstruction for tailed phages by Cryo-electron Microscopy. J. Structural Biology. (2025), 108262. == Abstract == The structure of the tailed phage is composed of an icosahedral (or elongated icosahedral) head and a spiral symmetrical tail, which are connected by a portal located at a unique vertex of the icosahedron. A series of image-processing method..." current
  • 08:4908:49, 29 December 2025 diff hist +98 Main Page →Reconstruction

22 December 2025

  • 08:3308:33, 22 December 2025 diff hist +1,424 N 2025Li Helicon Created page with "== Citation == Li, D., Zhang, X. and Jiang, W. 2025. Helicon: Helical parameter determination and 3D reconstruction from one image. J. Structural Biology. (2025), 108256. == Abstract == Helical symmetry is a common structural feature of many biological macromolecules. However, determination of the helical parameters and de novo 3D reconstruction remain challenging. We have developed a computational method, Helicon, which poses helical reconstruction as a linear regres..." current
  • 08:3208:32, 22 December 2025 diff hist +114 Main Page →Reconstruction

16 December 2025

  • 15:2215:22, 16 December 2025 diff hist +1,618 N 2025Kim Review Created page with "== Citation == Kim, H.-u., An, M.Y., Kim, Y.K., Chung, J.M. and Jung, H.S. 2025. Combining Cryo-EM with Computational Approaches To Revolutionize Structural Biology. The Protein Journal. (2025), 1–16. == Abstract == The development of cryo-electron microscopy (cryo-EM) has led to significant advancements in the field of structural biology. Specifically, improvements in both hardware and software for cryo-EM have not only addressed previously perceived limitations bu..." current
  • 15:2215:22, 16 December 2025 diff hist +95 Main Page →Books and reviews

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
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