User contributions for WikiSysop

Results for WikiSysop talk block log uploads logs
A user with 2,378 edits. Account created on 30 March 2009.
Jump to navigation Jump to search
Search for contributionsExpandCollapse
⧼contribs-top⧽
⧼contribs-date⧽
(newest | oldest) View ( | ) (20 | 50 | 100 | 250 | 500)

1 July 2025

  • 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
  • 09:5909:59, 20 June 2025 diff hist +1,341 N 2025Neiterman Frames Created page with "== Citation == E. H. Neiterman, A. Heimowitz, and G. Ben-Artzi, “A non-parametric approach to particle picking in all frames,” J. Structural Biology, p. 108201, 2025. == Abstract == Single-particle cryo-electron microscopy (cryo-EM) has significantly advanced macromolecular structure reconstruction. However, a key limitation is the conventional reliance on micrographs obtained by motion correction and averaging, which inherently loses the richness of information c..." current
  • 09:5809:58, 20 June 2025 diff hist +82 Main Page →Automatic particle picking
  • 09:4409:44, 20 June 2025 diff hist +1,717 N 2025Dickerson Damage Created page with "== Citation == J. L. Dickerson et al., “Reducing the effects of radiation damage in cryo-EM using liquid helium temperatures,” Proc. Natl. Academy of Sciences, vol. 122, no. 17, p. e2421538122, 2025. == Abstract == The physical limit in determining the atomic structure of biological molecules is radiation damage. In electron cryomicroscopy, there have been numerous attempts to reduce the effects of radiation damage by cooling the specimen beyond liquid-nitrogen te..." current
  • 09:4309:43, 20 June 2025 diff hist +96 Main Page →Image formation
  • 09:0109:01, 20 June 2025 diff hist +1,355 N 2025Kinman SIREN Created page with "== Citation == L. F. Kinman, M. V. Carreira, B. M. Powell, and J. H. Davis, “Automated model-free analysis of cryo-EM volume ensembles with SIREn,” Structure, vol. 33, no. 5, pp. 974–987, 2025. == Abstract == Cryogenic electron microscopy (cryo-EM) has the potential to capture snapshots of proteins in motion and generate hypotheses linking conformational states to biological function. This potential has been increasingly realized by the advent of machine learnin..." current
  • 09:0109:01, 20 June 2025 diff hist +96 Main Page →3D Heterogeneity

30 May 2025

  • 05:5105:51, 30 May 2025 diff hist +1,895 N 2025Mallet crAI Created page with "== Citation == V. Mallet, C. Rapisarda, H. Minoux, and M. Ovsjanikov, “Finding antibodies in cryo-EM maps with CrAI,” Bioinformatics, vol. 41, no. 5, p. btaf157, 2025. == Abstract == Motivation Therapeutic antibodies have emerged as a prominent class of new drugs due to their high specificity and their ability to bind to several protein targets. Once an initial antibody has been identified, its design and characteristics are refined using structural information, w..." current
  • 05:5005:50, 30 May 2025 diff hist +82 Main Page →Fitting and docking

16 May 2025

30 April 2025

  • 07:3307:33, 30 April 2025 diff hist +2,028 N 2020Zeng GumNet Created page with "== Citation == X. Zeng and M. Xu, “Gum-net: Unsupervised geometric matching for fast and accurate 3d subtomogram image alignment and averaging,” in Proc. of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2020, pp. 4073–4084. == Abstract == We propose a Geometric unsupervised matching Net- work (Gum-Net) for finding the geometric correspondence between two images with application to 3D subtomogram alignment and averaging. Subtomogram alignmen..." current
  • 07:3207:32, 30 April 2025 diff hist +86 Main Page →Subtomogram analysis

23 April 2025

  • 07:1207:12, 23 April 2025 diff hist +1,479 N 2025Harar FakET Created page with "== Citation == P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “Faket: Simulating cryo-electron tomograms with neural style transfer,” Structure, vol. 33, no. 4, pp. 820–827, 2025. == Abstract == In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce th..." current
  • 07:0407:04, 23 April 2025 diff hist +103 Main Page →Software

21 April 2025

  • 07:0007:00, 21 April 2025 diff hist +1,472 N 2025Schoennenbeck CryoVIA Created page with "== Citation == P. Schönnenbeck, B. Junglas, and C. Sachse, “CryoVIA: An image analysis toolkit for the quantification of membrane structures from cryo-EM micrographs,” Structure, 2025. == Abstract == Imaging of lipid structures and associated protein complexes using cryoelectron microscopy (cryo-EM) is a common visualization and structure determination technique. The quantitative analysis of the membrane structures, however, is not routine and time consuming in p..." current
  • 06:5906:59, 21 April 2025 diff hist +128 Main Page →Segmentation

16 April 2025

  • 10:4310:43, 16 April 2025 diff hist +1,827 N 2025Woollard InstaMap Created page with "== Citation == G. Woollard et al., “InstaMap: instant-NGP for cryo-EM density maps,” Biological Crystallography, vol. 81, no. 4, 2025. == Abstract == Despite the parallels between problems in computer vision and cryo-electron microscopy (cryo-EM), many state-of-the-art approaches from computer vision have yet to be adapted for cryo-EM. Within the computer-vision research community, implicits such as neural radiance fields (NeRFs) have enabled the detailed reconstr..." current
  • 10:4210:42, 16 April 2025 diff hist +93 Main Page →3D Reconstruction

15 April 2025

  • 15:2815:28, 15 April 2025 diff hist +1,226 N 2025Kapnulin Outlier Created page with "== Citation == L. Kapnulin, A. Heimowitz, and N. Sharon, “Outlier removal in cryo-EM via radial profiles,” J. Structural Biology, p. 108172, 2025. == Abstract == The process of particle picking, a crucial step in cryo-electron microscopy (cryo-EM) image analysis, often encounters challenges due to outliers, leading to inaccuracies in downstream processing. In response to this challenge, this research introduces an additional automated step to reduce the number of..." current
  • 15:2815:28, 15 April 2025 diff hist +87 Main Page →2D Alignment
  • 13:5813:58, 15 April 2025 diff hist +2,110 N 2025Chen GCTransNet Created page with "== Citation == C. Chen, Y. Yan, J. Wu, and W.-B. Gan, “GCTransNet: 3D mitochondrial instance segmentation based on Global Context Vision Transformers,” J. Structural Biology, p. 108170, 2025. == Abstract == Mitochondria are double membrane-bound organelles essential for generating energy in eukaryotic cells. Mitochondria can be readily visualized in 3D using Volume Electron Microscopy (vEM), and accurate image segmentation is vital for quantitative analysis of mit..." current
  • 13:5513:55, 15 April 2025 diff hist +113 Main Page →Segmentation
  • 13:5313:53, 15 April 2025 diff hist +2,551 N 2025Haynes OptimalIce Created page with "== Citation == R. M. Haynes, J. Myers, C. S. López, J. Evans, O. Davulcu, and C. Yoshioka, “A strategic approach for efficient cryo-EM grid optimization using design of experiments,” J. Structural Biology, vol. 217, no. 1, p. 108068, 2025. == Abstract == In recent years, cryo-electron microscopy (cryo-EM) has become a practical and effective method of determining structures at previously unattainable resolutions due to advances in detection, automation, and data..." current
  • 13:5213:52, 15 April 2025 diff hist +93 Main Page →Sample preparation

14 April 2025

  • 10:2910:29, 14 April 2025 diff hist +1,265 N 2023Shi Compression Created page with "== Citation == H. Shi, C. Wu, and X. Zhang, “Addressing compressive deformation of proteins embedded in crystalline ice,” Structure, vol. 31, no. 2, pp. 213–220, 2023. == Abstract == For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. Whether and how crystalline ice affects single-particle cryo-EM is still unclear. Here, s..." current
(newest | oldest) View ( | ) (20 | 50 | 100 | 250 | 500)
Retrieved from "https://3demmethods.i2pc.es/index.php/Special:Contributions/WikiSysop"