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A user with 2,486 edits. Account created on 30 March 2009.
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25 September 2025

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
  • 07:3507:35, 11 September 2025 diff hist +83 Main Page →Reconstruction
  • 07:2707:27, 11 September 2025 diff hist +2,046 N 2025Zheng Disorder 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..." current
  • 07:2507:25, 11 September 2025 diff hist +89 Main Page →Fitting and docking

29 August 2025

  • 09:3209:32, 29 August 2025 diff hist +1,857 N 2025Karolczak Ligand 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),..." current
  • 09:3209:32, 29 August 2025 diff hist +94 Main Page →Fitting and docking
  • 08:4408:44, 29 August 2025 diff hist +1,971 N 2024Jeon CryoBench 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..." current
  • 08:4408:44, 29 August 2025 diff hist +80 Main Page →Validation
  • 08:3908:39, 29 August 2025 diff hist +1,184 N 2024Bobe Calibration 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..." current
  • 08:3808:38, 29 August 2025 diff hist +70 Main Page →Automated data collection
  • 08:0708:07, 29 August 2025 diff hist +1,780 N 2025Haloi Ligand 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..." current
  • 08:0708:07, 29 August 2025 diff hist +118 Main Page →Fitting and docking
  • 07:5807:58, 29 August 2025 diff hist +2,363 N 2025Dingeldein 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..." current
  • 07:5707:57, 29 August 2025 diff hist +97 Main Page →3D Heterogeneity

28 August 2025

  • 09:5709:57, 28 August 2025 diff hist +1,397 N 2025Grant Nanodisc 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..." current
  • 09:5609:56, 28 August 2025 diff hist +93 Main Page →Sample preparation
  • 09:4309:43, 28 August 2025 diff hist +1,590 N 2025Herreros HetSiren 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..." current
  • 09:4209:42, 28 August 2025 diff hist +112 Main Page →3D Heterogeneity

27 August 2025

  • 10:1710:17, 27 August 2025 diff hist +1,392 N 2025Zhang Benchmark 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..." current
  • 10:1610:16, 27 August 2025 diff hist +119 Main Page →Fitting and docking

25 August 2025

  • 08:1208:12, 25 August 2025 diff hist +1,625 N 2025Levy CryoDRGNAI 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..." current
  • 08:1108:11, 25 August 2025 diff hist +125 Main Page →3D Heterogeneity

20 August 2025

  • 10:3810:38, 20 August 2025 diff hist +1,437 N 2019Kim CryoFit 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..." current
  • 10:3710:37, 20 August 2025 diff hist +73 Main Page →Fitting and docking
  • 10:1910:19, 20 August 2025 diff hist +1,853 N 2025Pintilie QScore 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..." current
  • 10:1810:18, 20 August 2025 diff hist +82 Main Page →Validation
  • 09:5409:54, 20 August 2025 diff hist +1,681 N 2025Zhang 2DTMpValue 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..." current
  • 09:5309:53, 20 August 2025 diff hist +95 Main Page →Automatic particle picking

11 August 2025

15 July 2025

  • 06:5306:53, 15 July 2025 diff hist +2,070 N 2025Van Probabilistic Created page with "== Citation == C. T. Van et al., “Probabilistic single-particle cryo-EM ab initio 3D reconstruction in SIMPLE,” Biological Crystallography, vol. 81, no. 8, 2025. == Abstract == Three-dimensional (3D) structure determination by single-particle analysis of cryo-electron microscopy (cryo-EM) images requires ab initio 3D reconstruction of density volume(s) from 2D images (particles). This large-scale inverse problem requires the determination of many million degrees o..." current
  • 06:5306:53, 15 July 2025 diff hist +95 Main Page →3D Reconstruction
  • 06:4206:42, 15 July 2025 diff hist +1,549 N 2025Zamanos CryoEMMAE Created page with "== Citation == A. Zamanos, P. Koromilas, G. Bouritsas, P. L. Kastritis, and Y. Panagakis, “Self-supervised learning for generalizable particle picking in cryo-EM micrographs,” Cell Reports Methods, 2025. == Abstract == We present cryoelectron microscopy masked autoencoder (cryo-EMMAE), a self-supervised method designed to overcome the need for manually annotated cryo-EM data. cryo-EMMAE leverages the representation space of a masked autoencoder to pick particle pi..." current
  • 06:4106:41, 15 July 2025 diff hist +101 Main Page →Automatic particle picking
  • 06:2906:29, 15 July 2025 diff hist +1,187 N 2025Wan Review Created page with "== Citation == W. Wan, “A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries,” Current Opinion in Structural Biology, vol. 93, p. 103116, 2025. == Abstract == Cryo-electron tomography (cryo-ET) enables 3D visualization of complex biological environments without the need for purification, thereby preserving the native biological context of the specimen. For determining macromolecular structures, repeating..." current
  • 06:2906:29, 15 July 2025 diff hist +107 Main Page →Books and reviews

14 July 2025

11 July 2025

  • 07:5407:54, 11 July 2025 diff hist +2,218 N 2025Wang E3CryoFold Created page with "== Citation == J. Wang, C. Tan, Z. Gao, G. Zhang, Y. Zhang, and S. Z. Li, “End-to-end Cryo-EM complex structure determination with high accuracy and ultra-fast speed,” Nature Machine Intelligence, pp. 1–13, 2025. == Abstract == While cryogenic-electron microscopy yields high-resolution density maps for complex structures, accurate determination of the corresponding atomic structures still necessitates significant expertise and labour-intensive manual interpretat..." current
  • 07:5407:54, 11 July 2025 diff hist +83 Main Page →Fitting and docking

10 July 2025

  • 06:3406:34, 10 July 2025 diff hist +1,560 N 2025Chen CryoCRAB Created page with "== Citation == Q. Chen et al., “A large-scale curated and filterable dataset for cryo-EM foundation model pre-training,” Scientific Data, vol. 12, no. 1, p. 960, 2025. == Abstract == Cryo-electron microscopy (cryo-EM) is a transformative imaging technology that enables near-atomic resolution 3D reconstruction of target biomolecule, playing a critical role in structural biology and drug discovery. Cryo-EM faces significant challenges due to its extremely low signal..." current
  • 06:3306:33, 10 July 2025 diff hist +89 Main Page →Software
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