New pages

20 February 2026

• 13:1713:17, 20 February 2026 2026Liu nextPYP (hist | edit) [2,111 bytes] Vilas (talk | contribs) (Created page with "== Citation == HF. Liu, Y. Zhou, Q. Huang, et al. In situ structure determination of conformationally flexible targets using nextPYP. Nat Protoc 21, 851–871 (2026). == Abstract == Single-particle cryoelectron tomography (SP-CET) is an imaging technique capable of determining the structure of proteins in their cellular environment at high-resolution. nextPYP is a web-based application designed to streamline the SP-CET structure determination process and facilitate t...")
• 12:5812:58, 20 February 2026 2026Schreiber Turonova TANGO (hist | edit) [1,538 bytes] Vilas (talk | contribs) (Created page with "== Citation == M. Schreiber, B. Turoňová, TANGO: Analysis and curation of particles in cryo-electron tomography. Nat Commun 17, 1557 (2026). == Abstract == Cryo-electron tomography (cryo-ET) enables the visualization of cellular structures in near-native environments, but its potential for spatial analysis has been underutilized due to a lack of versatile tools accommodating biological sample diversity. Available solutions often rely on case-specific or hypothesis...")
• 12:4312:43, 20 February 2026 2026JCarrion JDavis insituHet3D (hist | edit) [1,484 bytes] Vilas (talk | contribs) (Created page with "== Citation == J. Carrion, and J. Davis, "Resolving structural heterogeneity in situ through cryogenic electron tomography", Current Opinion in Structural Biology, Volume 96, 103188, 2026 == Abstract == Cryogenic electron tomography (cryoET) has emerged as a powerful tool for studying the structural heterogeneity of proteins and their complexes, offering insights into macromolecular dynamics directly within cells. Driven by recent computational advances, including pow...")
• 06:3506:35, 20 February 2026 2025Balanov Confirmation (hist | edit) [2,316 bytes] WikiSysop (talk | contribs) (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...")

18 February 2026

• 07:2607:26, 18 February 2026 2026Li Atomic (hist | edit) [1,122 bytes] WikiSysop (talk | contribs) (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...")

17 February 2026

• 04:5104:51, 17 February 2026 2026Chen CryoEvoBuild (hist | edit) [1,489 bytes] WikiSysop (talk | contribs) (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...")
• 04:3804:38, 17 February 2026 2026Urzhumtsev ProjDir (hist | edit) [1,148 bytes] WikiSysop (talk | contribs) (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...")
• 04:3004:30, 17 February 2026 2026Barchet NonUniform (hist | edit) [1,627 bytes] WikiSysop (talk | contribs) (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...")

13 February 2026

• 09:0409:04, 13 February 2026 2025Zhang CryoPROS (hist | edit) [1,480 bytes] WikiSysop (talk | contribs) (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...")
• 07:5807:58, 13 February 2026 2026Zhou Atomic (hist | edit) [677 bytes] WikiSysop (talk | contribs) (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...")

12 February 2026

• 08:5908:59, 12 February 2026 2025Mondal EMSequenceFinder (hist | edit) [2,467 bytes] WikiSysop (talk | contribs) (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...")
• 08:2508:25, 12 February 2026 2025Hansel Ligand (hist | edit) [2,201 bytes] WikiSysop (talk | contribs) (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...")

16 January 2026

• 15:4915:49, 16 January 2026 2025Yan Foundation (hist | edit) [1,266 bytes] WikiSysop (talk | contribs) (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...")
• 15:3715:37, 16 January 2026 2025Ma DeepTracer (hist | edit) [2,138 bytes] WikiSysop (talk | contribs) (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...")

9 January 2026

• 10:1610:16, 9 January 2026 2025Matinyan TRPX (hist | edit) [1,472 bytes] WikiSysop (talk | contribs) (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...")
• 08:3108:31, 9 January 2026 2026Heymann Ewald (hist | edit) [2,019 bytes] WikiSysop (talk | contribs) (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...")

7 January 2026

• 08:1408:14, 7 January 2026 2026Mulvaney CASP16 (hist | edit) [1,873 bytes] WikiSysop (talk | contribs) (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...")
• 08:0608:06, 7 January 2026 2025Tang CryoLike (hist | edit) [1,145 bytes] WikiSysop (talk | contribs) (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...")

30 December 2025

• 09:2509:25, 30 December 2025 2025Li EMProt (hist | edit) [1,381 bytes] WikiSysop (talk | contribs) (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-...")
• 08:4808:48, 30 December 2025 2025Leone Review (hist | edit) [1,320 bytes] WikiSysop (talk | contribs) (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...")

29 December 2025

• 14:3914:39, 29 December 2025 2025Sharma DataCollection (hist | edit) [1,454 bytes] Vilas (talk | contribs) (Created page with "== Citation == K. Sharma, M.J. Borgnia, "Advances in automation for cryo-electron tomography data collection", Current Opinion in Structural Biology, Volume 95, 103192, 2025 == Abstract == Cryo-electron microscopy has become the preferred method for determining structures of macromolecular complexes both in isolation, using single particle analysis, and in their cellular contexts, using cryo-electron tomography (Cryo-ET) combined with subvolume averaging (SVA). Collec...")
• 14:2914:29, 29 December 2025 2025Bartesaghi StrategiesHet3D (hist | edit) [1,389 bytes] Vilas (talk | contribs) (Created page with "== Citation == A. Bartesaghi, "Strategies for studying discrete heterogeneity in situ using cryo-electron tomography", Current Opinion in Structural Biology, Volume 95, 103186, 2025 == Abstract == Structural variability plays a crucial role in enabling biological function, as the ability of proteins to adopt multiple conformations allows them to perform diverse cellular tasks. Cryo-electron tomography combined with subtomogram averaging and classification has emerged...")
• 09:2909:29, 29 December 2025 2025Peng DiamTR (hist | edit) [1,871 bytes] WikiSysop (talk | contribs) (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...")
• 09:0209:02, 29 December 2025 2025Chen CryoEvoBuilding (hist | edit) [1,474 bytes] WikiSysop (talk | contribs) (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...")
• 08:5008:50, 29 December 2025 2025Chen Asymmetric (hist | edit) [1,938 bytes] WikiSysop (talk | contribs) (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...")

22 December 2025

• 08:3308:33, 22 December 2025 2025Li Helicon (hist | edit) [1,424 bytes] WikiSysop (talk | contribs) (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...")

16 December 2025

• 15:2215:22, 16 December 2025 2025Kim Review (hist | edit) [1,618 bytes] WikiSysop (talk | contribs) (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...")

21 November 2025

• 11:1411:14, 21 November 2025 2025Su CryoAtom (hist | edit) [1,681 bytes] WikiSysop (talk | contribs) (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...")
• 11:0711:07, 21 November 2025 2025Fu T2Relion (hist | edit) [1,535 bytes] WikiSysop (talk | contribs) (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...")