User contributions for WikiSysop

24 September 2026

• 05:1905:19, 24 September 2026 diff hist +2,081 N 2026Poudel CryoFSL Created page with "== Citation == Poudel, B., Gyawali, R., Dhakal, A., Cheng, J. and Xu, D. 2026. CryoFSL: an annotation-efficient, few-shot learning framework for robust protein particle picking in cryo-electron microscopy micrographs. Briefings in Bioinformatics. 27, 3 (2026), bbag285. == Abstract == Accurate identification of protein particles in cryo-electron microscopy (cryo-EM) micrographs is crucial for high-resolution structure determination, but remains challenging due to the h..." current
• 05:1805:18, 24 September 2026 diff hist +88 Main Page →Automatic particle picking
• 05:0205:02, 24 September 2026 diff hist +884 N 2021Chen Ewald Created page with "== Citation == Chen, J.P., Schmidt, K.E., Spence, J.C. and Kirian, R.A. 2021. A new solution to the curved Ewald sphere problem for 3D image reconstruction in electron microscopy. Ultramicroscopy. 224, (2021), 113234. == Abstract == We develop an algorithm capable of imaging a three-dimensional object given a collection of two-dimensional images of that object that are significantly influenced by the curvature of the Ewald sphere. These two-dimensional images cannot b..." current
• 05:0105:01, 24 September 2026 diff hist +83 Main Page →3D Reconstruction

18 September 2026

• 05:0805:08, 18 September 2026 diff hist +1,600 N 2026Burton PASR Created page with "== Citation == Burton Smith, R. and Murata, K. 2026. Post-acquisition super resolution for cryo-electron microscopy. IUCrJ. 13, 5 (2026). == Abstract == Recently, reports have demonstrated achieving resolutions beyond the physical Nyquist limit using super resolution acquisition. Here, we demonstrate exceeding this limitation by pre-processing the raw micrograph movies from counting mode data that have already reached the physical Nyquist reconstruction resolution. To..." current
• 05:0605:06, 18 September 2026 diff hist +71 Main Page →2D Preprocessing

17 September 2026

• 05:5405:54, 17 September 2026 diff hist +1,451 N 2026Klaholz Concepts Created page with "== Citation == Klaholz, B.P. 2026. A discussion of cryo-EM terminology as the outreach and number of PDB entries expand. IUCrJ. 13, 5 (2026). == Abstract == Cryo electron microscopy (cryo-EM) has made great advances in the last decade, progressively increasing its impact in structural biology as a key method to address molecular structures and mechanisms of various macromolecular complexes. Single-particle cryo-EM will soon equal the number of yearly entries in the Pr..." current
• 05:5305:53, 17 September 2026 diff hist +75 Main Page →Books and reviews

15 September 2026

• 09:1509:15, 15 September 2026 diff hist +1,625 N 2025Xu CryoDataBot Created page with "== Citation == Xu, Q., Wu, L., Rebelo, M., Feng, S., Yu, X., Farheen, F., Kihara, D. and Zhou, Z.H. 2025. CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology. GigaScience. 14, (2025), giaf127. == Abstract == Cryogenic electron microscopy (cryoEM) has revolutionized structural biology by enabling atomic-resolution visualization of biomacromolecules. With artificial intelligence (AI) increasing role in newly developed cryoEM tools, task-sp..." current
• 09:1409:14, 15 September 2026 diff hist +79 Main Page →Databases

3 September 2026

• 05:5705:57, 3 September 2026 diff hist +3,256 N 2026Sun QwenCryoMarker Created page with "== Citation == Sun, Y., Zhao, J., Xu, N., Wang, L., Ding, W. and Li, M. 2026. QwenCryoMarker: a universal post-processing framework for contamination-aware particle cleaning. Acta Crystallographica Sec. D. 82, 9 (2026). == Abstract == Cryo-electron microscopy (cryo-EM) micrographs are frequently contaminated by carbon edges, ice crystals, ethane bubbles and other high-contrast artifacts. These contaminants trigger abundant false positives in automated particle pickers..." current
• 05:5605:56, 3 September 2026 diff hist +107 Main Page →Automatic particle picking

31 August 2026

• 04:3704:37, 31 August 2026 diff hist +1,456 N 2026Kreymer EM Created page with "== Citation == Kreymer, S., Singer, A. and Bendory, T. 2026. Expectation-maximization for structure determination directly from cryo-em micrographs. Inverse problems and imaging. 27, (2026), 110. == Abstract == A single-particle cryo-electron microscopy (cryo- EM) measurement, called a micrograph, consists of multiple two-dimensional tomographic projections of a three-dimensional (3-D) molecular structure at unknown locations, taken under unknown viewing directions. A..." current
• 04:3604:36, 31 August 2026 diff hist +102 Main Page →3D Reconstruction

24 August 2026

• 05:1205:12, 24 August 2026 diff hist +1,760 N 2026Jain ProtAcid Created page with "== Citation == Jain, A., Cao, K. and Kihara, D. 2026. Computational approaches for protein–DNA/RNA complex modeling for Cryo-EM maps. Current Protocols. 6, 8 (2026), e70409. == Abstract == Cryogenic electron microscopy (cryo-EM) has become a key method in structural biology for determining macromolecular structures. Numerous computational tools have been developed to build atomic models from cryo-EM density maps. However, relatively few tools are available for model..." current
• 05:1105:11, 24 August 2026 diff hist +122 Main Page →Fitting and docking

21 August 2026

• 05:3705:37, 21 August 2026 diff hist +1,146 N 2025Schafer CryoSift Created page with "== Citation == Schäfer, J.-H., Calza, A., Hom, K., Damodar, P., Peng, R., Bogdanović, N., Lander, G.C., Stagg, S.M. and Cianfrocco, M.A. 2025. CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection. Acta Crystallographica Sec. F. 81, 12 (2025), 517–526. == Abstract == Single-particle cryo-electron microscopy (cryo-EM) has become an essential tool in structural biology. However, automating repetitive tasks remains an ongoing challenge..." current
• 05:3605:36, 21 August 2026 diff hist +86 Main Page →2D Classification and clustering
• 05:2905:29, 21 August 2026 diff hist +1,801 N 2025Shugaeva Prior Created page with "== Citation == Shugaeva, T., Howard, R.J., Haloi, N. and Lindahl, E. 2025. Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulations. Communications Chemistry. 8, 1 (2025), 317. == Abstract == Modeling atomic coordinates into a target cryo-electron microscopy map is a crucial step in structure determination. Despite recent advances, proteins with multiple functional states remain a challenge - particularly when suita..." current
• 05:2905:29, 21 August 2026 diff hist +112 Main Page →Fitting and docking
• 05:2105:21, 21 August 2026 diff hist +1,465 N 2025Zhang Struct2MapGAN Created page with "== Citation == Zhang, C., Condon, A. and Dao Duc, K. 2025. Struc2mapGAN: improving synthetic cryogenic electron microscopy density maps with generative adversarial networks. Bioinformatics advances. 5, 1 (2025), vbaf179. == Abstract == Motivation Generating synthetic cryogenic electron microscopy 3D density maps from molecular structures has potential important applications in structural biology. Yet existing simulation-based methods cannot mimic all the complex featu..." current
• 05:2005:20, 21 August 2026 diff hist +109 Main Page →Fitting and docking
• 05:1105:11, 21 August 2026 diff hist +1,555 N 2026Wankowicz Atomic Created page with "== Citation == Wankowicz, S.A. and Bonomi, M. 2026. From possibility to precision in macromolecular ensemble prediction. Nature Methods. (2026), 1–9. == Abstract == Proteins and other macromolecules exist as dynamic ensembles of interconverting conformations essential for catalysis, allosteric regulation and molecular recognition. While AI tools like AlphaFold have revolutionized static structure prediction, they cannot yet capture conformational ensembles. Progress..." current
• 05:1005:10, 21 August 2026 diff hist +70 Main Page →Books and reviews

20 August 2026

• 08:5308:53, 20 August 2026 diff hist +1,822 N 2022Dickerson InelasticContribution Created page with "== Citation == Dickerson, J.L. and Russo, C.J. 2022. Phase contrast imaging with inelastically scattered electrons from any layer of a thick specimen. Ultramicroscopy. 237, (2022), 113511. == Abstract == A controversy exists as to whether the signal in a high resolution phase contrast electron micrograph of a particle in a thick specimen is the same irrespective of the particle’s position along the beam axis. Different conceptions of inelastic scattering and its eff..." current
• 08:4008:40, 20 August 2026 diff hist +114 Main Page →Image formation
• 05:1205:12, 20 August 2026 diff hist +1,866 N 2026Fadini Rocket Created page with "== Citation == Fadini, A., Li, M., McCoy, A.J., Banjara, S., Okumura, H., Napier, E., Fontana, P., Khan, A.R., Jovine, L., Terwilliger, T.C. and others 2026. AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network. Nature methods. 23, (2026), 785–795. == Abstract == Advances in machine learning have transformed structural biology, enabling swift and accurate prediction of protein structure from sequence. However, key cha..." current
• 05:1105:11, 20 August 2026 diff hist +89 Main Page →Fitting and docking

13 August 2026

• 06:3706:37, 13 August 2026 diff hist +1,700 N 2025Gyawali Multimodal Created page with "== Citation == Gyawali, R., Dhakal, A. and Cheng, J. 2025. Multimodal deep learning integration of cryo-EM and AlphaFold3 for high-accuracy protein structure determination. Communications Chemistry. 8, 1 (2025), 320. == Abstract == Cryo-electron microscopy (cryo-EM) is a key technology for determining the structures of proteins, particularly large protein complexes. However, automatically building high-accuracy protein structures from cryo-EM density maps remains a cr..." current
• 06:3706:37, 13 August 2026 diff hist +80 Main Page →Fitting and docking
• 06:3206:32, 13 August 2026 diff hist +1,113 N 2026Savas Distogram Created page with "== Citation == Savaş, B., Barlas, A.B. and Karaca, E. 2026. Exploring the potential of AlphaFold distograms for predicting binding-induced hinge motions. FEBS letters. 600, 10 (2026), 1558–1570. == Abstract == AlphaFold models provide static structural predictions, limiting their use in interpreting flexible regions in low-resolution cryo-EM maps. Here, we assess whether AlphaFold-generated distograms can instead reveal conformational flexibility, focusing on bindi..." current
• 06:3206:32, 13 August 2026 diff hist +114 Main Page →Fitting and docking
• 06:2506:25, 13 August 2026 diff hist +1,831 N 2025Alexadrescu Mix Created page with "== Citation == Alexandrescu, L., Lessin, W. and Lander, G.C. 2025. Mix-it-up’: accessible time-resolved cryo-EM on the millisecond timescale. IUCrJ. 12, 6 (2025), 710–724. == Abstract == Biological reactions often involve macromolecules that undergo substrate-induced conformational changes in under a second, yet capturing these transient states remains challenging. While high-resolution structural techniques such as X-ray crystallography and cryo-electron microsco..." current
• 06:2406:24, 13 August 2026 diff hist +119 Main Page →Sample preparation
• 06:1806:18, 13 August 2026 diff hist +1,984 N 2025Toader SGD Created page with "== Citation == Toader, B., Brubaker, M.A. and Lederman, R.R. 2025. Efficient high-resolution refinement in cryo-EM with stochastic gradient descent. Acta Crystallographica Sec. D. 81, (2025), 327–343. == Abstract == Electron cryo-microscopy (cryo-EM) is an imaging technique that is widely used in structural biology to determine the three-dimensional structure of biological molecules from noisy two-dimensional projections with unknown orientations. As the typical pip..." current
• 06:1706:17, 13 August 2026 diff hist +87 Main Page →3D Reconstruction
• 06:1106:11, 13 August 2026 diff hist +2,052 N 2026Balanov Confirmation Created page with "== Citation == Balanov, A., Huleihel, W. and Bendory, T. 2026. Einstein from noise: Statistical analysis. IEEE Transactions on Signal Processing. 74, (2026), 1751–1766. == Abstract == “Einstein from noise” (EfN) is a prominent example of the model bias phenomenon, where systematic errors in the statistical model lead to spurious but consistent estimates. In the EfN experiment, one falsely believes that a set of observations contains noisy, shifted copies of a te..." current
• 06:0906:09, 13 August 2026 diff hist +84 Main Page →Automatic particle picking

12 August 2026

• 04:3704:37, 12 August 2026 diff hist +5 Main Page →3D Reconstruction
• 04:3604:36, 12 August 2026 diff hist +1,836 N 2025Zhang CryoFastAR Created page with "== Citation == Zhang, J., Zhou, S., Dai, H., Liu, X., Wang, P., Fan, Z., Pei, Y. and Yu, J. 2025. CryoFastAR: Fast Cryo-EM Ab Initio Reconstruction Made Easy. 2025 IEEE/CVF International Conference on Computer Vision (ICCV) (2025), 8462–8471. == Abstract == Pose estimation from unordered images is fundamental for 3D reconstruction, robotics, and scientific imaging. Recent geometric foundation models, such as DUSt3R, enable end-to-end dense 3D reconstruction but rema..." current
• 04:3504:35, 12 August 2026 diff hist +90 Main Page →3D Reconstruction
• 04:1904:19, 12 August 2026 diff hist +2,052 N 2026Balanov Einstein Created page with "== Citation == Balanov, A., Huleihel, W. and Bendory, T. 2026. Einstein from noise: Statistical analysis. IEEE Transactions on Signal Processing. 74, (2026), 1751–1766. == Abstract == “Einstein from noise” (EfN) is a prominent example of the model bias phenomenon, where systematic errors in the statistical model lead to spurious but consistent estimates. In the EfN experiment, one falsely believes that a set of observations contains noisy, shifted copies of a te..." current
• 04:1804:18, 12 August 2026 diff hist +101 Main Page →2D Alignment

11 August 2026

• 05:2805:28, 11 August 2026 diff hist +2,369 N 2026Fromm LowDose Created page with "== Citation == Fromm, S.A. and Mattei, S. 2026. LowDoseWizard–rapid and standardised setup of low-dose cryo-TEM imaging in SerialEM. Acta Crystallographica Sec. D. 82, (2026), 990–997. == Abstract == Structure elucidation of biological macromolecules by single-particle cryogenic electron microscopy (SPA cryo-EM) or cryogenic electron tomography (cryo- ET) relies on low-dose imaging on cryogenic transmission electron microscopes (cryo-TEMs). Routine microscope setu..." current
• 05:2605:26, 11 August 2026 diff hist +68 Main Page →Automated data collection

10 August 2026

• 05:1305:13, 10 August 2026 diff hist +2,350 N 2026Marchan Unattended Created page with "== Citation == Marchán Torres, D., Conesa, P., Garcia, A., Iceta, M., Broche, L., Gragera, M., Linares, R., Kwong, H.S., Chichón, F.J., Svensson, O. and others 2026. An unattended image-processing pipeline for on-the-fly quality assessment and 3D exploration in cryo-EM. Acta Crystallographica Sec. D. 82, 8 (2026). == Abstract == Single-particle analysis (SPA) by cryogenic electron microscopy (cryo-EM) has become a cornerstone of structural biology; yet, the workflow..." current
• 05:1205:12, 10 August 2026 diff hist +102 Main Page →Software

7 August 2026

• 11:0811:08, 7 August 2026 diff hist +1,827 N 2026Van Polar Created page with "== Citation == Van, C.T., Reboul, C.F., Caesar, J.J., Meana-Pañeda, R. and Elmlund, H. 2026. A polar Fourier geometric approach to volume-free single-particle 3D reconstruction. IUCrJ. 13, 4 (2026). == Abstract == We introduce a compact mathematical formulation for the inverse singleparticle 3D reconstruction problem, a high-dimensional inverse problem in which millions of parameters are estimated from extremely noisy experimental measurements. Given a collection of..." current
• 11:0511:05, 7 August 2026 diff hist +90 Main Page →3D Alignment

23 July 2026

• 06:3106:31, 23 July 2026 diff hist +1,350 N 2013Ruskin DQE Created page with "== Citation == Ruskin, A.I., Yu, Z. and Grigorieff, N. 2013. Quantitative characterization of electron detectors for transmission electron microscopy. J. Structural biology. 184, 3 (2013), 385–393. == Abstract == A new generation of direct electron detectors for transmission electron microscopy (TEM) promises significant improvement over previous detectors in terms of their modulation transfer function (MTF) and detective quantum efficiency (DQE). However, the perfo..." current