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A user with 2,507 edits. Account created on 30 March 2009.
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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 current
  • 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
  • 06:2706:27, 23 July 2026 diff hist +112 Main Page →Image formation
  • 06:1906:19, 23 July 2026 diff hist +979 N 2026Motta Dublins Created page with "== Citation == Motta Alves, G., Andrews, T., McBean, P., Wells, T., El-Gomati, M.M., Burkhalter, S., Schulze-Briese, C., Zambon, P., McMullan, G., Henderson, R. and others 2026. The Dublin lens: a Cc= 1.0 mm objective lens intended for CryoEM at 100 keV. Methods in Microscopy. 3, 1 (2026), 19–25. == Abstract == We have designed, fabricated and tested a lens with a chromatic aberration coefficient (Cc) of 1.0 mm, a 4.0 mm pole-gap and 2.0 mm bore that is wide enough..." current
  • 06:1806:18, 23 July 2026 diff hist +73 Main Page →Image formation

22 July 2026

  • 06:4606:46, 22 July 2026 diff hist +1,782 N 2024Wang CryoSeek Created page with "== Citation == Wang, T., Li, Z., Xu, K., Huang, W., Huang, G., Zhang, Q.C. and Yan, N. 2024. CryoSeek: A strategy for bioentity discovery using cryoelectron microscopy. Proceedings of the National Academy of Sciences. 121, 42 (2024), e2417046121. == Abstract == Structural biology is experiencing a paradigm shift from targeted structural determination to structure-guided discovery of previously uncharacterized bioentities. We employed cryoelectron microscopy (cryo-EM)..." current
  • 06:4606:46, 22 July 2026 diff hist +117 Main Page →Software

9 July 2026

  • 06:4306:43, 9 July 2026 diff hist +1,309 N 2026Petrov Laser Created page with "== Citation == Petrov, P.N., Zhang, J.T., Remis, J., Axelrod, J.J., Cheng, H., Cooper, E.S., Hicklin, I.K., Sandhaus, S., Schnurr, C., Glaeser, R.M. and others 2026. Laser phase plate improves structure determination of small proteins by cryo-EM. Science. (2026), eaeh0665. == Abstract == Phase plates can in principle overcome the poor image contrast in electron cryo–microscopy (cryo-EM) and the resulting limits on the structural reconstruction of small proteins. How..." current
  • 06:4206:42, 9 July 2026 diff hist +57 Main Page →Image formation
  • 06:2406:24, 9 July 2026 diff hist +1,201 N 2026Subramaniam Review Created page with "== Citation == Subramaniam, S., Kühlbrandt, W. and Henderson, R. 2026. Cryo-EM: the revolution continues. IUCrJ. 13, 4 (2026). == Abstract == The near-universal adoption of electron cryo-microscopy (cryo-EM) by structural and cell biologists has led to exponential growth of the field, especially over the last two decades, with a doubling in the number of deposited electronmicroscopy density maps every 2.5 years. This exponential growth has changed in recent years to..." current
  • 06:2406:24, 9 July 2026 diff hist +81 Main Page →Books and reviews

7 July 2026

  • 06:3106:31, 7 July 2026 diff hist +1,648 N 2026Chrencik SBDD Created page with "== Citation == Chrencik, J.E., Su, H.-P., Gomez Llorente, Y., Palte, R.L., Klein, D.J., Hayes, R.P., Antine, S.P., Asmar-Rovira, G.A., Bertoletti, N., Byrne, N.J. and others 2026. The evolving role of structural biology in pharma: integration of X-ray crystallography, cryo-electron microscopy and beyond. Biological Crystallography. 82, 6 (2026). == Abstract == Structural biology has fundamentally influenced pharmaceutical research and development at Merck Sharp & Dohm..." current
  • 06:3006:30, 7 July 2026 diff hist +89 Main Page →Books and reviews
  • 06:1706:17, 7 July 2026 diff hist +1,461 N 2025Starynska Membrane Created page with "== Citation == Starynska, A., Cameron, C.J., Sigworth, F.J. and Tagare, H.D. 2026. Automated Membrane Detection and Subtraction for Structure Determination of Membrane Proteins in Cryogenic Electron Microscopy. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (2026), 6553–6562. == Abstract == High-resolution cryo-electron microscopy (cryo-EM) reconstruction of membrane proteins often requires the bilayer membrane containing the prote..." current
  • 06:1606:16, 7 July 2026 diff hist +97 Main Page →2D Preprocessing
  • 05:5505:55, 7 July 2026 diff hist +1,599 N 2026Gao CryoKRAQEN Created page with "== Citation == Gao, W., Wu, Y. and He, X. 2026. CryoKRAQEN: Kernel-Regularized Annealing for Quantized Embedding Networks in Cryo-EM Heterogeneous Reconstruction. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (2026), 28298–28307. == Abstract == Heterogeneous reconstruction in cryo-electron microscopy (Cryo-EM) is fundamental for understanding macromolecular structural diversity, yet remains challenging due to extreme noise, contin..." current
  • 05:5405:54, 7 July 2026 diff hist +159 Main Page →3D Heterogeneity

2 June 2026

  • 06:5806:58, 2 June 2026 diff hist +2,958 N 2026Behkamal Secondary Created page with "== Citation == Behkamal, B., Etemadheravi, M.P., Mahmoodjanloo, A., Mansoori, A., Naghibzadeh, M., Al Nasr, K. and Saberi, M.R. 2026. A Novel Machine-Learning Based Method for Resolving Secondary Structure Topology in Medium-Resolution Cryo-EM Density Maps. Intl. J. of Molecular Sciences. 27, 10 (2026), 4388. == Abstract == Medium-resolution cryo-electron microscopy (cryo-EM) density maps preserve substantial information about protein secondary-structure organization;..." current
  • 06:5706:57, 2 June 2026 diff hist +107 Main Page →Fitting and docking
  • 06:1606:16, 2 June 2026 diff hist +1,218 N 2026Kwon Elastic Created page with "== Citation == Kwon, M.C. and Abrahams, J.P. 2026. Elastic and Inelastic Interactions of Electrons in Transmission Electron Microscopy. Ultramicroscopy. (2026), 114383. == Abstract == High-energy electrons passing through a sample in a transmission electron microscope carry structural information through their interactions with the sample’s atoms. Elastically scattered electrons, which undergo no significant energy loss, convey spatial details in their scattering an..." current
  • 06:1506:15, 2 June 2026 diff hist +80 Main Page →Books and reviews

26 May 2026

  • 05:5405:54, 26 May 2026 diff hist +1,640 N 2026Obrien CryoJax Created page with "== Citation == O’Brien, M.J., Silva-Sánchez, D., Woollard, G., Je, K., Hanson, S.M., Needleman, D.J., Cossio, P., Thiede, E.H. and Astore, M.A. 2026. CryoJAX: a cryo-electron microscopy image-simulation library in JAX. Acta Crystallographica Sec. D. 82, 3 (2026). == Abstract == While cryo-electron microscopy (cryo-EM) has come to prominence in the last decade due to its ability to resolve biomolecular complexes at atomic resolution, advancements in experimental and..." current
  • 05:5405:54, 26 May 2026 diff hist +98 Main Page →Image formation

25 May 2026

  • 06:0606:06, 25 May 2026 diff hist +1,697 N 2025Evans LowDim Created page with "== Citation == Evans, L., Murad, O.-V., Dingeldein, L., Cossio, P., Covino, R. and Meila, M. 2025. Cryo-EM images are intrinsically low dimensional. PRX Life. 3, 3 (2025), 33025. == Abstract == Simulation-based inference provides a powerful framework for cryoelectron microscopy, employing neural networks in methods like CryoSBI to infer biomolecular conformations via learned latent representations. This latent space represents a rich opportunity, encoding valuable inf..." current
  • 06:0606:06, 25 May 2026 diff hist +83 Main Page →Image formation

22 May 2026

  • 06:3206:32, 22 May 2026 diff hist +2,278 N 2026Silva CryoJax Created page with "== Citation == Silva-Sánchez, D., Berezuk, A.M., Zhu, X., Thiede, E.H., Lederman, R.R. and Cossio, P. 2026. Cryo-Electron Microscopy Structural Ensemble Optimization Using Individual Particles. J. of Chemical Theory and Computation. (2026). == Abstract == Biomolecules are inherently dynamic, transitioning between various conformational states to execute their biological functions; consequently, characterizing their ensemble distributions (the population of these conf..." current
  • 06:3006:30, 22 May 2026 diff hist +111 Main Page →3D Heterogeneity

16 May 2026

13 May 2026

  • 06:5206:52, 13 May 2026 diff hist +1,980 N 2026Premaraj DualJet Created page with "== Citation == Premaraj, N., Huysmans, P., Ploum, M., Schijns, L., Peters, P.J., López-Iglesias, C., Ravelli, R.B. and Knoops, K. 2026. An experimental platform for exploring dual-jet vitrification mechanisms in cryo-EM sample preparation. Methods in Microscopy. 0 (2026). == Abstract == Jet vitrification harnesses the exceptionally high cooling potential of rapidly moving liquid cryogens to achieve ultrafast sample freezing with superior cooling efficiency. Building..." current
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