User contributions for WikiSysop

20 February 2026

• 06:3506:35, 20 February 2026 diff hist +2,316 N 2025Balanov Confirmation Created page with "== Citation == Balanov, A., Bendory, T. and Huleihel, W. 2025. Confirmation bias in Gaussian mixture models. IEEE Trans. on Information Theory. (2025). == Abstract == Confirmation bias, the tendency to interpret information in a way that aligns with one’s preconceptions, can profoundly impact scientific research, leading to conclusions that reflect the researcher’s hypotheses even when the observational data do not support them. This issue is especially critical i..." current
• 06:3406:34, 20 February 2026 diff hist +72 Main Page →2D Alignment

18 February 2026

• 07:2607:26, 18 February 2026 diff hist +1,122 N 2026Li Atomic Created page with "== Citation == Li, T. and Huang, S.-Y. 2026. Deep learning–based postprocessing and model building for cryo-electron microscopy maps. Current Opinion in Structural Biology. 96, (2026), 103196. == Abstract == Cryo-electron microscopy (cryo-EM) has emerged as one of the most powerful techniques for determining the structures of biological macromolecules. The ultimate goal of cryo-EM is to determine the atomic structure of target molecules, where map postprocessing and..." current
• 07:2407:24, 18 February 2026 diff hist +109 Main Page →Books and reviews

17 February 2026

• 04:5104:51, 17 February 2026 diff hist +1,489 N 2026Chen CryoEvoBuild Created page with "== Citation == Chen, J., Li, T., He, J. and Huang, S.-Y. 2026. Protein model building for intermediate-resolution cryo-EM maps by integrating evolutionary and experimental information. Structure. 34, (2026), 375–384. == 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 p..." current
• 04:5004:50, 17 February 2026 diff hist +109 Main Page →Fitting and docking
• 04:3804:38, 17 February 2026 diff hist +1,148 N 2026Urzhumtsev ProjDir Created page with "== Citation == Urzhumtsev, A.G. 2026. Quantifying distributions of cryo-EM projections. Biological Crystallography. 82, 2 (2026). == Abstract == In cryo-electron microscopy, a set of two-dimensional projections collected from different viewing directions may complicate image processing and subsequent model building if the distribution of these views is non-uniform. View distributions are traditionally represented as color-coded two-dimensional diagrams. However, such..." current
• 04:3804:38, 17 February 2026 diff hist +115 Main Page →Validation
• 04:3004:30, 17 February 2026 diff hist +1,627 N 2026Barchet NonUniform Created page with "== Citation == Barchet, C., von Loeffelholz, O., Bahena-Ceron, R., Klaholz, B.P. and Urzhumtsev, A.G. 2026. Explicit correction of severely non-uniform distributions of cryo-EM views. Biological Crystallography. 82, 2 (2026). == Abstract == The quality of three-dimensional macromolecular image reconstruction by cryo electron microscopy (cryo-EM) strongly depends on the number and the quality of the respective two-dimensional projections and on their angular distributi..." current
• 04:2904:29, 17 February 2026 diff hist +109 Main Page →3D Reconstruction

13 February 2026

• 09:0409:04, 13 February 2026 diff hist +1,480 N 2025Zhang CryoPROS Created page with "== Citation == Zhang, H., Zheng, D., Wu, Q., Yan, N., Peng, H., Hu, Q., Peng, Y., Yan, Z., Shi, Z., Bao, C. and others 2025. CryoPROS: Correcting misalignment caused by preferred orientation using AI-generated auxiliary particles. Nature Communications. 16, 1 (2025), 4565. == Abstract == The preferred orientation phenomenon is a common issue in cryo-EM, posing a persistent challenge to conventional reconstruction methods. In this study, we introduce cryoPROS, a comput..." current
• 09:0309:03, 13 February 2026 diff hist +106 Main Page →3D Reconstruction
• 07:5807:58, 13 February 2026 diff hist +677 N 2026Zhou Atomic Created page with "== Citation == Zhou, X., Xu, X. and Zhang, G. 2026. When cryo-EM modeling meets structure prediction: Structural biology technologies. Nature Structural & Molecular Biology. (2026), 1–3. == Abstract == Accurately interpreting density maps into atomic models is a central yet challenging goal of cryo-EM. Two studies now reveal distinct ways in which protein structure prediction can be incorporated into cryo-EM model building to enable more accurate and robust automate..." current
• 07:5807:58, 13 February 2026 diff hist 0 Main Page →Books and reviews
• 07:5707:57, 13 February 2026 diff hist +90 Main Page →Books and reviews

12 February 2026

• 08:5908:59, 12 February 2026 diff hist +2,467 N 2025Mondal EMSequenceFinder Created page with "== Citation == Mondal, D., Kumar, V., Satler, T., Ramachandran, R., Saltzberg, D., Chemmama, I., Pilla, K.B., Echeverria, I., Webb, B.M., Gupta, M. and others 2025. Recognizing amino acid sidechains in a medium-resolution cryo-electron density map. Protein Science. 34, 8 (2025), e70217. == Abstract == Building an accurate atomic structure model of a protein into a cryo-electron microscopy (cryo-EM) map at worse than 3 Å resolution is difficult. To facilitate this t..." current
• 08:5808:58, 12 February 2026 diff hist +128 Main Page →Fitting and docking
• 08:2508:25, 12 February 2026 diff hist +2,201 N 2025Hansel Ligand Created page with "== Citation == Hansel-Harris, A.T., Tillack, A.F., Santos-Martins, D., Holcomb, M. and Forli, S. 2025. Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance. Protein Science. 34, 3 (2025), e70082. == Abstract == Recent advances in structural biology have led to the publication of a wealth of high-resolution x-ray crystallography (XRC) and cryo-EM macromolecule structures, including many complexe..." current
• 08:2408:24, 12 February 2026 diff hist +92 Main Page →Fitting and docking

16 January 2026

• 15:4915:49, 16 January 2026 diff hist +1,266 N 2025Yan Foundation Created page with "== Citation == Yan, Y., Fan, S., Yuan, F. and Shen, H. 2025. A comprehensive foundation model for cryo-EM image processing. Nature Methods. 23, (2025), 88–95. == Abstract == Cryogenic electron microscopy (cryo-EM) has become a premier technique for determining high-resolution structures of biological macromolecules. However, its broad application is constrained by the demand for specialized expertise. Here, to address this limitation, we introduce the Cryo-EM Image..." current
• 15:4815:48, 16 January 2026 diff hist +118 Main Page →2D Preprocessing
• 15:3715:37, 16 January 2026 diff hist +2,138 N 2025Ma DeepTracer Created page with "== Citation == Ma, X. and Si, D. 2025. Beyond current boundaries: Integrating deep learning and AlphaFold for enhanced protein structure prediction from low-resolution cryo-EM maps. Computational Biology and Chemistry. 119, (2025), 108494. == Abstract == Constructing atomic models from cryo-electron microscopy (cryo-EM) maps is a crucial yet intricate task in structural biology. While advancements in deep learning, such as convolutional neural networks (CNNs) and grap..." current
• 15:3615:36, 16 January 2026 diff hist +100 Main Page →Fitting and docking

9 January 2026

• 10:1610:16, 9 January 2026 diff hist +1,472 N 2025Matinyan TRPX Created page with "== Citation == Matinyan, S., Filipcik, P., Waterman, D., Owen, C. and Abrahams, J. 2025. TRPXv2. 0: superfast, parallel compression of diffraction patterns and images, with native Python and HDF5 support. Ultramicroscopy. (2025), 114298. == Abstract == Scientific data in structural biology are being produced faster and in larger volumes than can be comfortably stored, processed, or shared. To address this challenge, we introduced the next generation TERSE/PROLIX (TRPX..." current
• 10:1610:16, 9 January 2026 diff hist +78 Main Page →Software
• 08:3108:31, 9 January 2026 diff hist +2,019 N 2026Heymann Ewald Created page with "== Citation == Heymann, J.B. 2026. The relationship between the Ewald sphere and exit wave explored using focal series electron micrographs. IUCrJ. 13, 1 (2026). == Abstract == CryoEM reconstructions must be performed along the Ewald spheres to achieve resolutions beyond the projection approximation limit. The linear theory of image formation models the scattering from the specimen and focusing by the objective lens as two conjugate Ewald spheres that correspond to th..." current
• 08:3008:30, 9 January 2026 diff hist +144 Main Page →Image formation

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
• 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

• 13:4613:46, 12 December 2025 diff hist +175 Main Page →Online courses and Learning material

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