New pages

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...")

17:2417:24, 14 November 2025 2024Shekarforoush CryoSPIN (hist | edit) [1,667 bytes] WikiSysop (talk | contribs) (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...")
17:0317:03, 14 November 2025 2024Wang CommonLines (hist | edit) [1,755 bytes] WikiSysop (talk | contribs) (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...")

09:2109:21, 13 November 2025 2025Chen GMM (hist | edit) [1,138 bytes] WikiSysop (talk | contribs) (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...")
09:0709:07, 13 November 2025 2025Selvaraj CryoTEN (hist | edit) [1,975 bytes] WikiSysop (talk | contribs) (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...")
08:3708:37, 13 November 2025 2025Bromberg Hand (hist | edit) [1,496 bytes] WikiSysop (talk | contribs) (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...")

17:3217:32, 12 November 2025 2025Dhakal Benchmark (hist | edit) [1,671 bytes] WikiSysop (talk | contribs) (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...")
16:5316:53, 12 November 2025 2025Urzhumtsev RescaleFSC (hist | edit) [1,543 bytes] WikiSysop (talk | contribs) (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...")
16:3316:33, 12 November 2025 2025Morales Membranes (hist | edit) [1,815 bytes] WikiSysop (talk | contribs) (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...")

14:0414:04, 6 November 2025 2025Gusach Diffusion (hist | edit) [1,367 bytes] WikiSysop (talk | contribs) (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...")

23:3123:31, 5 November 2025 2025Ni GTPick (hist | edit) [1,530 bytes] WikiSysop (talk | contribs) (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...")

22:4322:43, 2 November 2025 2025Elad Review (hist | edit) [1,495 bytes] WikiSysop (talk | contribs) (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...")
22:2622:26, 2 November 2025 2025Muenks EmeraldID (hist | edit) [1,494 bytes] WikiSysop (talk | contribs) (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...")
21:3521:35, 2 November 2025 2025Li validation (hist | edit) [1,458 bytes] WikiSysop (talk | contribs) (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...")
21:2821:28, 2 November 2025 2025Lauzirika Distinguishable (hist | edit) [1,395 bytes] WikiSysop (talk | contribs) (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...")
21:1021:10, 2 November 2025 2025Luo DiffFit (hist | edit) [2,335 bytes] WikiSysop (talk | contribs) (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...")

14:4714:47, 16 October 2025 2025Roth ArtiaX (hist | edit) [1,658 bytes] Vilas (talk | contribs) (Created page with "== Citation == P. Roth, U.H. Ermel, D. Moser, G. Arctaedius, M. Wehrheim, M.P. Scheffer, A.S. Frangakis, ArtiaX: geometric models, camera paths and image processing tools, Journal of Structural Biology, 217, 3, 2025. == Abstract == Biomolecular image analysis and data interpretation is significantly improved through the application of advanced visualization techniques. Numerous visualization packages are currently available, spanning a broad spectrum of applications....")
12:4512:45, 16 October 2025 2025Chen Detergent (hist | edit) [1,732 bytes] WikiSysop (talk | contribs) (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...")

16:3116:31, 29 September 2025 2025Chung CRISP (hist | edit) [2,267 bytes] WikiSysop (talk | contribs) (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...")

06:1406:14, 25 September 2025 2020Ma RotationInvariant (hist | edit) [1,720 bytes] WikiSysop (talk | contribs) (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...")
05:5605:56, 25 September 2025 2023Cesa Alignment (hist | edit) [1,810 bytes] WikiSysop (talk | contribs) (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...")

16:2316:23, 22 September 2025 2025Matsuoka ForceConstant (hist | edit) [1,915 bytes] WikiSysop (talk | contribs) (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...")

07:4707:47, 11 September 2025 2025Khoshbin Magellon (hist | edit) [1,792 bytes] WikiSysop (talk | contribs) (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...")
07:3507:35, 11 September 2025 2025 Huang (hist | edit) [1,488 bytes] WikiSysop (talk | contribs) (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...")
07:2707:27, 11 September 2025 2025Zheng Disorder (hist | edit) [2,046 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Zheng, S. 2025. Exploring the Bottleneck in Cryo-EM Dynamic Disorder Feature and Advanced Hybrid Prediction Model. Biophysica. 5, 3 (2025), 39. == Abstract == Cryo-electron microscopy single-particle analysis (cryo-EM SPA) has advanced threedimensional protein structure determination, yet resolving intrinsically disordered proteins and regions (IDPs/IDRs) remains challenging due to conformational heterogeneity. This research evaluates cryo-EM’s capaci...")

09:3209:32, 29 August 2025 2025Karolczak Ligand (hist | edit) [1,857 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Karolczak, J., Przybyłowska, A., Szewczyk, K., Taisner, W., Heumann, J.M., Stowell, M.H., Nowicki, M. and Brzezinski, D. 2025. Ligand identification in CryoEM and X-ray maps using deep learning. Bioinformatics. 41, 1 (2025), btae749. == Abstract == Motivation: Accurately identifying ligands plays a crucial role in the process of structure-guided drug design. Based on density maps from X-ray diffraction or cryogenic-sample electron microscopy (cryoEM),...")
08:4408:44, 29 August 2025 2024Jeon CryoBench (hist | edit) [1,971 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Jeon, M., Raghu, R., Astore, M., Woollard, G., Feathers, J., Kaz, A., Hanson, S., Cossio, P. and Zhong, E. 2024. CryoBench: Diverse and challenging datasets for the heterogeneity problem in cryo-EM. Advances in Neural Information Processing Systems. 37, (2024), 89468–89512. == Abstract == Cryo-electron microscopy (cryo-EM) is a powerful technique for determining high-resolution 3D biomolecular structures from imaging data. Its unique ability to captur...")
08:3908:39, 29 August 2025 2024Bobe Calibration (hist | edit) [1,184 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Bobe, D., Kopylov, M., Miller, J., Owji, A.P. and Eng, E.T. 2024. Multi-species cryoEM calibration and workflow verification standard. Structural Biology and Crystallization Communications. 80, 11 (2024), 320–327. == Abstract == Cryogenic electron microscopy (cryoEM) is a rapidly growing structural biology modality that has been successful in revealing molecular details of biological systems. However, unlike established biophysical and analytical tech...")
08:0708:07, 29 August 2025 2025Haloi Ligand (hist | edit) [1,780 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Haloi, N., Howard, R.J. and Lindahl, E. 2025. Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics. PLOS Computational Biology. 21, 8 (2025), e1013367. == Abstract == Resolving protein-ligand interactions in atomic detail is key to understanding how small molecules regulate macromolecular function. Although recent breakthroughs in cryogenic electron microscopy (cryo-EM) have enabled high-quality reconstruction of numerous complex b...")
07:5807:58, 29 August 2025 2025Dingeldein (hist | edit) [2,363 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Dingeldein, L., Silva-Sánchez, D., Evans, L., D’Imprima, E., Grigorieff, N., Covino, R. and Cossio, P. 2025. Amortized template matching of molecular conformations from cryoelectron microscopy images using simulation-based inference. Proceedings of the National Academy of Sciences. 122, 23 (2025), e2420158122. == Abstract == Characterizing the conformational ensemble of biomolecular systems is key to understand their functions. Cryoelectron microscop...")

09:5709:57, 28 August 2025 2025Grant Nanodisc (hist | edit) [1,397 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Grant, A.J. and Schmidt-Krey, I. 2025. Nanodisc-reconstitution for single particle cryo-EM structure determination of membrane proteins. Current Opinion in Structural Biology. 93, (2025), 103072. == Abstract == Reconstitution of membrane proteins in nanodiscs has proven to be a highly effective approach to study membrane protein structures in a lipid bilayer, resulting in many recent single particle cryo-EM structures. While most of these studies employ...")
09:4309:43, 28 August 2025 2025Herreros HetSiren (hist | edit) [1,590 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Herreros, D., Mata, C.P., Noddings, C., Irene, D., Krieger, J., Agard, D.A., Tsai, M.-D., Sorzano, C.O.S. and Carazo, J.M. 2025. Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN. Nature communications. 16, 1 (2025), 3751. == Abstract == Single-particle analysis by Cryo-electron microscopy (CryoEM) provides direct access to the conformations of macromolecules. Traditional methods assum...")

10:1710:17, 27 August 2025 2025Zhang Benchmark (hist | edit) [1,392 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Zhang, C., Condon, A. and Dao Duc, K. 2025. A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps. Briefings in Bioinformatics. 26, 4 (2025), bbaf322. == Abstract == Advancements in deep learning (DL) have recently led to new methods for automated construction of atomic models of proteins, from single-particle cryogenic electron microscopy (cryo-EM) density maps. We condu...")

08:1208:12, 25 August 2025 2025Levy CryoDRGNAI (hist | edit) [1,625 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Levy, A., Raghu, R., Feathers, J.R., Grzadkowski, M., Poitevin, F., Johnston, J.D., Vallese, F., Clarke, O.B., Wetzstein, G. and Zhong, E.D. 2025. CryoDRGN-AI: neural ab initio reconstruction of challenging cryo-EM and cryo-ET datasets. Nature Methods. (2025), 1–9. == Abstract == Proteins and other biomolecules form dynamic macromolecular machines that are tightly orchestrated to move, bind and perform chemistry. Cryo-electron microscopy and cryo-elec...")

10:3810:38, 20 August 2025 2019Kim CryoFit (hist | edit) [1,437 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Kim, D.N., Moriarty, N.W., Kirmizialtin, S., Afonine, P.V., Poon, B., Sobolev, O.V., Adams, P.D. and Sanbonmatsu, K. 2019. Cryo_fit: Democratization of flexible fitting for cryo-EM. Journal of structural biology. 208, 1 (2019), 1–6. == Abstract == Cryo-electron microscopy (cryo-EM) is becoming a method of choice for describing native conformations of biomolecular complexes at high resolution. The rapid growth of cryo-EM in recent years has created a h...")
10:1910:19, 20 August 2025 2025Pintilie QScore (hist | edit) [1,853 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Pintilie, G., Shao, C., Wang, Z., Hudson, B.P., Flatt, J.W., Schmid, M.F., Morris, K., Burley, S.K. and Chiu, W. 2025. Q-score as a reliability measure for protein, nucleic acid, and small molecule atomic coordinate models derived from 3DEM density maps. Structure. D81, (2025), 410–422. == Abstract == Atomic coordinate models are important for the interpretation of 3D maps produced with cryoEM and cryoET (3D electron microscopy; 3DEM). In addition to...")
09:5409:54, 20 August 2025 2025Zhang 2DTMpValue (hist | edit) [1,681 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Zhang, K., Cossio, P., Rangan, A.V., Lucas, B.A. and Grigorieff, N. 2025. A new statistical metric for robust target detection in cryo-EM using 2D template matching. IUCrJ. 12, 2 (2025). == Abstract == 2D template matching (2DTM) can be used to detect molecules and their assemblies in cellular cryo-EM images with high positional and orientational accuracy. While 2DTM successfully detects spherical targets such as large ribosomal subunits, challenges rem...")

New pages

21 November 2025

14 November 2025

13 November 2025

12 November 2025

6 November 2025

5 November 2025

2 November 2025

16 October 2025

29 September 2025

25 September 2025

22 September 2025

11 September 2025

29 August 2025

28 August 2025

27 August 2025

25 August 2025

20 August 2025

Navigation menu

Search