Main public logs

Combined display of all available logs of 3DEM-Methods. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).

• 06:07, 17 September 2025 WikiSysop talk contribs created page User talk:Vilas (Welcome!)
• 06:07, 17 September 2025 WikiSysop talk contribs created page User:Vilas (Creating user page for new user.)
• 06:07, 17 September 2025 User account Vilas talk contribs was created by WikiSysop talk contribs and password was sent by email (One more editor)
• 07:47, 11 September 2025 WikiSysop talk contribs created page 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...")
• 07:35, 11 September 2025 WikiSysop talk contribs created page 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...")
• 07:27, 11 September 2025 WikiSysop talk contribs created page 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...")
• 09:32, 29 August 2025 WikiSysop talk contribs created page 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),...")
• 08:44, 29 August 2025 WikiSysop talk contribs created page 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...")
• 08:39, 29 August 2025 WikiSysop talk contribs created page 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...")
• 08:07, 29 August 2025 WikiSysop talk contribs created page 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...")
• 07:58, 29 August 2025 WikiSysop talk contribs created page 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...")
• 09:57, 28 August 2025 WikiSysop talk contribs created page 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...")
• 09:43, 28 August 2025 WikiSysop talk contribs created page 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...")
• 10:17, 27 August 2025 WikiSysop talk contribs created page 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...")
• 08:12, 25 August 2025 WikiSysop talk contribs created page 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...")
• 09:11, 21 August 2025 WikiSysop talk contribs unblocked 169.254.2.101 talk
• 10:38, 20 August 2025 WikiSysop talk contribs created page 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...")
• 10:19, 20 August 2025 WikiSysop talk contribs created page 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...")
• 09:54, 20 August 2025 WikiSysop talk contribs created page 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...")
• 22:06, 13 August 2025 WikiSysop talk contribs blocked 169.254.2.101 talk with an expiration time of indefinite (anonymous users only, account creation disabled)
• 09:45, 11 August 2025 WikiSysop talk contribs created page User talk:Mikeltxo (Welcome!)
• 09:45, 11 August 2025 WikiSysop talk contribs created page User:Mikeltxo (Creating user page for new user.)
• 09:45, 11 August 2025 User account Mikeltxo talk contribs was created by WikiSysop talk contribs and password was sent by email (Cuenta para Mikel)
• 06:53, 15 July 2025 WikiSysop talk contribs created page 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...")
• 06:42, 15 July 2025 WikiSysop talk contribs created page 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...")
• 06:29, 15 July 2025 WikiSysop talk contribs created page 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...")
• 07:43, 14 July 2025 WikiSysop talk contribs created page 2025Shub Mic (Created page with "== Citation == L. Shub, W. Liu, G. Skiniotis, M. J. Keiser, and M. J. Robertson, “MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures,” Nature Communications, vol. 16, no. 1, p. 6182, 2025. == Abstract == At sufficiently high resolution, x-ray crystallography and cryogenic electron microscopy are capable of resolving small spherical map features corresponding to either water or ions. Correct classification of these sites provi...")
• 07:54, 11 July 2025 WikiSysop talk contribs created page 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...")
• 06:34, 10 July 2025 WikiSysop talk contribs created page 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...")
• 07:13, 8 July 2025 WikiSysop talk contribs created page 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...")
• 07:05, 8 July 2025 WikiSysop talk contribs created page 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...")
• 06:54, 8 July 2025 WikiSysop talk contribs created page 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...")
• 06:46, 1 July 2025 WikiSysop talk contribs created page 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...")
• 06:40, 1 July 2025 WikiSysop talk contribs created page 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...")
• 06:59, 30 June 2025 WikiSysop talk contribs created page 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...")
• 08:06, 25 June 2025 WikiSysop talk contribs created page 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...")
• 05:57, 25 June 2025 WikiSysop talk contribs created page 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...")
• 06:32, 24 June 2025 WikiSysop talk contribs created page 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...")
• 06:24, 24 June 2025 WikiSysop talk contribs created page 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...")
• 06:19, 24 June 2025 WikiSysop talk contribs created page 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...")
• 10:37, 20 June 2025 WikiSysop talk contribs created page 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...")
• 10:30, 20 June 2025 WikiSysop talk contribs created page 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...")
• 10:26, 20 June 2025 WikiSysop talk contribs created page 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...")
• 10:13, 20 June 2025 WikiSysop talk contribs created page 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...")
• 10:05, 20 June 2025 WikiSysop talk contribs created page 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...")
• 09:59, 20 June 2025 WikiSysop talk contribs created page 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...")
• 09:44, 20 June 2025 WikiSysop talk contribs created page 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...")
• 09:01, 20 June 2025 WikiSysop talk contribs created page 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...")
• 05:51, 30 May 2025 WikiSysop talk contribs created page 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...")
• 06:04, 16 May 2025 WikiSysop talk contribs created page 2024Levy Hydra (Created page with "== Citation == A. Levy et al., “Mixture of neural fields for heterogeneous reconstruction in cryo-EM,” Advances in Neural Information Processing Systems, vol. 37, pp. 56988–57017, 2024. == Abstract == Cryo-electron microscopy (cryo-EM) is an experimental technique for protein structure determination that images an ensemble of macromolecules in near-physiological contexts. While recent advances enable the reconstruction of dynamic conformations of a single biomol...")