User contributions for WikiSysop

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A user with 2,404 edits. Account created on 30 March 2009.
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20 August 2025

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

8 July 2025

  • 07:1307:13, 8 July 2025 diff hist +2,088 N 2025Gilles Covariance Created page with "== Citation == M. A. Gilles and A. Singer, “Cryo-EM heterogeneity analysis using regularized covariance estimation and kernel regression,” Proc. Natl. Academy of Sciences, vol. 122, no. 9, p. e2419140122, 2025. == Abstract == Proteins and the complexes they form are central to nearly all cellular processes. Their flexibility, expressed through a continuum of states, provides a window into their biological functions. Cryogenic electron microscopy (cryo-EM) is an id..." current
  • 07:1107:11, 8 July 2025 diff hist +139 Main Page →3D Heterogeneity
  • 07:0507:05, 8 July 2025 diff hist +1,819 N 2025Chaillet PytomMatchPick Created page with "== Citation == M. L. Chaillet, S. Roet, R. C. Veltkamp, and F. Förster, “pytom-match-pick: a tophat-transform constraint for automated classification in template matching,” J. Structural Biology X, p. 100125, 2025. == Abstract == Template matching (TM) in cryo-electron tomography (cryo-ET) enables in situ detection and localization of known macromolecules. However, TM faces challenges of weak signal of the macromolecules and interfering features with a high signa..." current
  • 07:0407:04, 8 July 2025 diff hist +96 Main Page →Subtomogram analysis
  • 06:5406:54, 8 July 2025 diff hist +1,211 N 2025Bai NUDFT Created page with "== Citation == Z. Bai and J. Huang, “Non-uniform Fourier transform based image classification in single-particle Cryo-EM,” J. Structural Biology X, p. 100121, 2025. == Abstract == In the single-particle Cryo-EM projection image classification, it is a common practice to apply the Fourier transform to the images and extract rotation-invariant features in the frequency domain. However, this process involves interpolation, which can reduce the accuracy of the results..." current
  • 06:5406:54, 8 July 2025 diff hist +87 Main Page →2D Classification and clustering

1 July 2025

  • 06:4606:46, 1 July 2025 diff hist +2,355 N 2025Carr Map2Seq Created page with "== Citation == K. D. Carr et al., “Protein identification using cryo-EM and artificial intelligence guides improved sample purification,” Journal of Structural Biology: X, p. 100120, 2025. == Abstract == Protein purification is essential in protein biochemistry, structural biology, and protein design, enabling the determination of protein structures, the study of biological mechanisms, and the characterization of both natural and de novo designed proteins. However..." current
  • 06:4506:45, 1 July 2025 diff hist +63 Main Page →Fitting and docking
  • 06:4006:40, 1 July 2025 diff hist +2,487 N 2025Wu ZeroLossCCCorrected Created page with "== Citation == J. Wu et al., “Chromatic aberration (Cc) corrected cryo-EM: the structure of pseudorabies virus (PRV) using both zero-loss and energy loss electrons,” Ultramicroscopy, p. 114182, 2025. == Abstract == Here we have investigated the potential improvement in imaging vitrified biological specimens with the help of a chromatic aberration (Cc)-corrector. Using a newly developed chromatic aberration-corrected electron cryomicroscope (cryo-EM), the phase con..." current
  • 06:3906:39, 1 July 2025 diff hist +117 Main Page →Image formation

30 June 2025

  • 06:5906:59, 30 June 2025 diff hist +993 N 2025Patwardhan Extending Created page with "== Citation == A. Patwardhan, R. Henderson, and C. J. Russo, “Extending the reach of single-particle cryoEM.,” Current Opinion in Structural Biology, p. 103005, 2025. == Abstract == Molecular structure determination using electron cryomicroscopy (cryoEM) is poised in early 2025 to surpass X-ray crystallography as the most used method for experimentally determining new structures. But the technique has not reached the physical limits set by radiation damage and the..." current
  • 06:5806:58, 30 June 2025 diff hist +128 Main Page →Books and reviews

25 June 2025

  • 08:0608:06, 25 June 2025 diff hist +1,818 N 2025Singh Mismatch Created page with "== Citation == P. K. Singh and T. Iverson, “Improving CryoEM maps of symmetry-mismatched macromolecular assemblies: A case study on the flagellar motor,” J. Structural Biology, vol. 217, no. 2, p. 108184, 2025. == Abstract == Advances in cryo-electron microscopy instrumentation and sample preparation have significantly improved the ability to collect quality data for biomolecular structures. However, achieving resolutions consistent with data quality remains chall..." current
  • 08:0508:05, 25 June 2025 diff hist +112 Main Page →3D Reconstruction
  • 05:5705:57, 25 June 2025 diff hist +1,466 N 2025Wan CryoETStandards Created page with "== Citation == W. Wan, “A case for community metadata standards in cryo-electron tomography,” Emerging Topics in Life Sciences, vol. 9, no. 01, p. ETLS20240013, 2025. == Abstract == In the past decade, cryo-electron microscopy and single particle analysis (SPA) have quickly become key methods in structural biology. In particular, increased access to equipment and streamlined software has enabled new users to successfully carry out SPA projects. At the same time, c..." current
  • 05:5505:55, 25 June 2025 diff hist +89 Main Page →Books and reviews

24 June 2025

  • 06:3206:32, 24 June 2025 diff hist +1,368 N 2025Riahi EMPOT Created page with "== Citation == A. Tajmir Riahi, C. Zhang, A. Condon, J. Chen, and K. Dao Duc, “Alignment of Partially Overlapping Cryo-EM Maps Using Unbalanced Gromov-Wasserstein Divergence,” PRX Life, vol. 3, no. 2, p. 23003, 2025. == Abstract == Aligning EM density maps and fitting atomic models are essential steps in single-particle cryogenic electron microscopy (cryo-em), with recent methods leveraging various algorithms and machine learning tools. As aligning maps remains ch..." current
  • 06:2906:29, 24 June 2025 diff hist +127 Main Page →Fitting and docking
  • 06:2406:24, 24 June 2025 diff hist +1,658 N 2025Zhan AITom Created page with "== Citation == X. Zhan, X. Zeng, M. R. Uddin, and M. Xu, “AITom: AI-guided cryo-electron tomography image analyses toolkit,” Journal of Structural Biology, p. 108207, 2025. == Abstract == Cryo-electron tomography (cryo-ET) is an essential tool in structural biology, uniquely capable of visualizing three-dimensional macromolecular complexes within their native cellular environments, thereby providing profound molecular-level insights. Despite its significant promis..." current
  • 06:2306:23, 24 June 2025 diff hist +77 Main Page →Software
  • 06:1906:19, 24 June 2025 diff hist +1,643 N 2025Zhang Emol Created page with "== Citation == Z. Zhang, L. Xu, S. Zhang, C. Peng, G. Zhang, and X. Zhou, “EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation,” Nucleic Acids Research, p. gkaf416, 2025. == Abstract == Atomic str uct ure modeling is a cr ucial step in determining the str uct ures of protein comple x es using cry o-electron microscop y (cry o-EM). T his work introduces DEMO-EMol, an improved server that integrat..." current
  • 06:1806:18, 24 June 2025 diff hist +109 Main Page →Fitting and docking

20 June 2025

  • 10:3710:37, 20 June 2025 diff hist +1,150 N 2025Chen GMMs Created page with "== Citation == M. Chen, “Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks,” Communications Biology, vol. 8, no. 1, pp. 1–9, 2025. == 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 w..." current
  • 10:3710:37, 20 June 2025 diff hist +72 Main Page →Fitting and docking
  • 10:3010:30, 20 June 2025 diff hist +1,657 N 2025Guo Alignment Created page with "== Citation == S. Guo, Z. Xu, X. Li, Z. Yang, C. Feng, and R. Han, “Robust projection parameter calibration in cryo-ET with L1-norm optimization,” Ultramicroscopy, p. 114134, 2025. == Abstract == Fiducial marker-based alignment in cryo-electron tomography (cryo-ET) has been extensively studied over a long period. The calibration of projection parameters using nonlinear least squares technique methodologies stands as the ultimate and pivotal stage in the alignment..." current
  • 10:3010:30, 20 June 2025 diff hist +87 Main Page →Image alignment
  • 10:2610:26, 20 June 2025 diff hist +945 N 2025Martinez Review Created page with "== Citation == A. Martinez-Sanchez, “Template matching and machine learning for cryo-electron tomography,” Current Opinion in Structural Biology, vol. 93, p. 103058, 2025. == Abstract == Cryo-electron tomography is the best-suited imaging technique for visual proteomics. Recent advances have increased the number, quality, and resolution of tomograms. However, object detection is the bottleneck task of the analysis workflow because, so far, only a few molecules can..." current
  • 10:2610:26, 20 June 2025 diff hist +92 Main Page →Books and reviews
  • 10:1310:13, 20 June 2025 diff hist +1,826 N 2025Khavnekar PSD Created page with "== Citation == S. Khavnekar and W. Wan, “An approach for coherent periodogram averaging of tilt-series data for improved contrast transfer function estimation,” FEBS Open Bio, 2025. == Abstract == Cryo-electron microscopy (cryo-EM) has become an indispensable technique for determining three-dimensional structures of biological macromolecules. A critical aspect of achieving high-resolution cryo-EM reconstructions is accurately determining and correcting for the mic..." current
  • 10:1210:12, 20 June 2025 diff hist +81 Main Page →CTF estimation and restoration
  • 10:0510:05, 20 June 2025 diff hist +1,725 N 2025Kiewisz ProjectionSynthesis Created page with "== Citation == R. Kiewisz, G. Meyer-Lee, and T. Bepler, “A latent back-projection network for novel projection synthesis for improved Cryo-ET,” in ICLR 2025 Workshop on Generative and Experimental Perspectives for Biomolecular Design, == Abstract == Cryo-electron tomography (Cryo-ET) is hindered by the missing wedge, a gap in Fourier-space information caused by limited tilt-series angular coverage, leading to anisotropic resolution loss and artifacts. Current meth..." current
  • 10:0410:04, 20 June 2025 diff hist +123 Main Page →Missing-wedge correction
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