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).

• 06:36, 20 January 2025 WikiSysop talk contribs created page 2025Debarnot IceTide (Created page with "== Citation == V. Debarnot, V. Kishore, R. D. Righetto, and I. Dokmanic, “Ice-tide: Implicit cryo-et imaging and deformation estimation,” IEEE Transactions on Computational Imaging, vol. 11, pp. 24–35, 2025. == Abstract == We introduce ICE-TIDE, amethod for cryogenic electron tomography (cryo-ET) that simultaneously aligns observations and reconstructs a high-resolution volume. The alignment of tilt series in cryo-ET is a major problem limiting the resolution of...")
• 17:28, 17 January 2025 WikiSysop talk contribs created page 2025Elferich CTFFind5 (Created page with "== Citation == J. Elferich, L. Kong, X. Zottig, and N. Grigorieff, “CTFFIND5 provides improved insight into quality, tilt, and thickness of TEM samples,” eLife, vol. 13, p. RP97227, 2024. == Abstract == Images taken by transmission electron microscopes are usually affected by lens aberrations and image defocus, among other factors. These distortions can be modeled in reciprocal space using the contrast transfer function (CTF). Accurate estimation and correction of...")
• 17:20, 17 January 2025 WikiSysop talk contribs created page 2024Zhang Kam (Created page with "== Citation == A. Zhang et al., “Moment-based metrics for molecules computable from cryogenic electron microscopy images,” Biological Imaging, vol. 4, p. e3, 2024. == Abstract == Single-particle cryogenic electron microscopy (cryo-EM) is an imaging technique capable of recovering the high-resolution three-dimensional (3D) structure of biological macromolecules from many noisy and randomly oriented projection images. One notable approach to 3D reconstruction, known...")
• 09:47, 14 January 2025 WikiSysop talk contribs created page 2024Sanchez Cesped (Created page with "== Citation == R. Sanchez-Garcia, M. Saur, J. Vargas, C. Poelking, and C. M. Deane, “CESPED: A benchmark for supervised particle pose estimation in cryo-EM,” Physical Review Research, vol. 6, no. 2, p. 23245, 2024. == Abstract == Cryo-EM is a powerful tool for understanding macromolecular structures, yet current methods for structure reconstruction are slow and computationally demanding. To accelerate research on pose estimation, we present CESPED, a data set spec...")
• 08:02, 3 January 2025 WikiSysop talk contribs created page 2023Lucas Baited (Created page with "== Citation == B. A. Lucas, B. A. Himes, and N. Grigorieff, “Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias,” Elife, vol. 12, p. RP90486, 2023. == Abstract == Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and c...")
• 07:55, 3 January 2025 WikiSysop talk contribs created page 2024Bhattacharjee TimeResolved (Created page with "== Citation == S. Bhattacharjee et al., “Time resolution in cryo-EM using a PDMS-based microfluidic chip assembly and its application to the study of HflX-mediated ribosome recycling,” Cell, vol. 187, no. 3, pp. 782–796, 2024. == Abstract == The rapid kinetics of biological processes and associated short-lived conformational changes pose a significant challenge in attempts to structurally visualize biomolecules during a reaction in real time. Conventionally, on-...")
• 07:50, 3 January 2025 WikiSysop talk contribs created page 2024Tuijtel Lamellae (Created page with "== Citation == M. W. Tuijtel et al., “Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging,” Science Advances, vol. 10, no. 17, p. eadk6285, 2024. == Abstract == Cryo–electron tomography (cryo-ET) is a powerful method to elucidate subcellular architecture and to structurally analyze biomolecules in situ by subtomogram averaging, yet data quality critically depends on specimen thickness. Cells that are too thick for transmission imagin...")
• 07:45, 3 January 2025 WikiSysop talk contribs created page 2023Grassetti Graphene (Created page with "== Citation == A. V. Grassetti, M. B. May, and J. H. Davis, “Enhancing CryoEM Sample Preparation Using Graphene Monolayer on Microscopy Grids (Video)| JoVE,” JoVE (Journal of Visualized Experiments), no. 201, p. e66023, 2023. == Abstract == In cryogenic electron microscopy (cryoEM), purified macromolecules are applied to a grid bearing a holey carbon foil; the molecules are then blotted to remove excess liquid and rapidly frozen in a roughly 20-100 nm thick layer...")
• 07:58, 27 December 2024 WikiSysop talk contribs created page 2023DiIorio AbInitio (Created page with "== Citation == M. C. DiIorio and A. W. Kulczyk, “Novel artificial intelligence-based approaches for ab initio structure determination and atomic model building for cryo-electron microscopy,” Micromachines, vol. 14, no. 9, p. 1674, 2023. == Abstract == Single particle cryo-electron microscopy (cryo-EM) has emerged as the prevailing method for near-atomic structure determination, shedding light on the important molecular mechanisms of biological macromolecules. Howe...")
• 07:53, 27 December 2024 WikiSysop talk contribs created page 2023Langeberg RNAScaffold (Created page with "== Citation == C. J. Langeberg and J. S. Kieft, “A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM,” Nucleic Acids Research, vol. 51, no. 20, pp. e100–e100, 2023. == Abstract == Single-particle cryo-electron microscopy (cryo-EM) can reveal the structures of large and often dynamic molecules, but smaller biomolecules remain challenging targets due to their intrinsic low signal to noise ratio. Methods to resolve small proteins...")
• 07:37, 27 December 2024 WikiSysop talk contribs created page 2023Riahi Transport (Created page with "== Citation == A. T. Riahi, G. Woollard, F. Poitevin, A. Condon, and K. D. Duc, “Alignot: An optimal transport based algorithm for fast 3d alignment with applications to cryogenic electron microscopy density maps,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023. == Abstract == Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step re...")
• 07:19, 27 December 2024 WikiSysop talk contribs created page 2024Singer Wasserstein (Created page with "== Citation == A. Singer and R. Yang, “Alignment of density maps in Wasserstein distance,” Biological Imaging, vol. 4, p. e5, 2024. == Abstract == In this article, we propose an algorithm for aligning three-dimensional objects when represented as density maps, motivated by applications in cryogenic electron microscopy. The algorithm is based on minimizing the 1-Wasserstein distance between the density maps after a rigid transformation. The induced loss function en...")
• 11:01, 26 December 2024 WikiSysop talk contribs created page 2023Forsberg Filter (Created page with "== Citation == B. O. Forsberg, P. N. Shah, and A. Burt, “A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps,” Nature Communications, vol. 14, no. 1, p. 5802, 2023. == Abstract == Cryo electron microscopy (cryo-EM) is used by biological research to visualize biomolecular complexes in 3D, but the heterogeneity of cryo-EM reconstructions is not easily estimated. Current processing paradigms nevertheless exert great eff...")
• 10:50, 26 December 2024 WikiSysop talk contribs created page 2023Dai CryoFEM (Created page with "== Citation == X. Dai, L. Wu, S. Yoo, and Q. Liu, “Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps,” Briefings in Bioinformatics, vol. 24, no. 6, p. bbad405, 2023. == Abstract == Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3-D atomic models of biological molecules. AlphaFold-predicted models generate initial 3-D coordinates; however, model inaccuracy and conformational heterogeneity o...")
• 10:44, 26 December 2024 WikiSysop talk contribs created page 2023Afonine Varref (Created page with "== Citation == P. V. Afonine, A. Gobet, L. Moissonnier, J. Martin, B. K. Poon, and V. Chaptal, “Conformational space exploration of cryo-EM structures by variability refinement,” Biochimica et Biophysica Acta (BBA)-Biomembranes, vol. 1865, no. 4, p. 184133, 2023. == Abstract == Cryo-EM observation of biological samples enables visualization of sample heterogeneity, in the form of discrete states that are separable, or continuous heterogeneity as a result of local...")
• 10:40, 26 December 2024 WikiSysop talk contribs created page 2023Yee Ot2Rec (Created page with "== Citation == N. B.-y. Yee, E. M. Ho, M. Darrow, and M. Basham, “Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow,” Biophysical Journal, vol. 122, no. 3, p. 462a, 2023. == Abstract == Electron cryo-tomography is an imaging technique for probing 3D structures with at the nanometer scale. This technique has been used extensively in the biomedical field to study the complex structures of proteins and other macromolecules. With...")
• 20:13, 23 December 2024 WikiSysop talk contribs created page 2023Zhang Denoising (Created page with "== Citation == D. Zhang et al., “Unsupervised Cryo-EM Images Denoising and Clustering based on Deep Convolutional Autoencoder and K-Means++,” IEEE Trans. Medical Imaging, vol. 42, pp. 1509–1521, 2023. == Abstract == Cryo-electron microscopy (cryo-EM) is a widely used structural determination technique. Because of the extremely low signal-to-noise ratio (SNR) of images captured by cryo-EM, clustering single-particle cryo-EM images with high accuracy is challengin...")
• 20:03, 23 December 2024 WikiSysop talk contribs created page 2024Bendory Complexity (Created page with "== Citation == T. Bendory and D. Edidin, “The Sample Complexity of Sparse Multireference Alignment and Single-Particle Cryo-Electron Microscopy,” SIAM J. on Mathematics of Data Science, vol. 6, no. 2, pp. 254–282, 2024. == Abstract == Multireference alignment (MRA) is the problem of recovering a signal from its multiple noisy copies, each acted upon by a random group element. MRA is mainly motivated by single-particle cryo–electron microscopy (cryo-EM) that ha...")
• 19:58, 23 December 2024 WikiSysop talk contribs created page 2024Liu DeepETPicker (Created page with "== Citation == G. Liu, T. Niu, M. Qiu, Y. Zhu, F. Sun, and G. Yang, “DeepETPicker: Fast and accurate 3D particle picking for cryo-electron tomography using weakly supervised deep learning,” Nature Communications, vol. 15, no. 1, p. 2090, 2024. == Abstract == To solve three-dimensional structures of biological macromolecules in situ, large numbers of particles often need to be picked from cryo-electron tomograms. However, adoption of automated particle-picking meth...")
• 19:54, 23 December 2024 WikiSysop talk contribs created page 2023Rice TomoTwin (Created page with "== Citation == G. Rice, T. Wagner, M. Stabrin, O. Sitsel, D. Prumbaum, and S. Raunser, “TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining,” Nature methods, vol. 20, no. 6, pp. 871–880, 2023. == Abstract == Cryogenic-electron tomography enables the visualization of cellular environments in extreme detail, however, tools to analyze the full amount of information contained within these densely packed volu...")
• 19:50, 23 December 2024 WikiSysop talk contribs created page 2023Weiss Noise (Created page with "== Citation == G. Weiss-Dicker, A. Eldar, Y. Shkolinsky, and T. Bendory, “Unsupervised particle sorting for cryo-EM using probabilistic PCA,” in 2023 IEEE 20th Intl. Symposium on Biomedical Imaging (ISBI), IEEE, 2023, pp. 1–5. == Abstract == Single-particle cryo-electron microscopy (cryo-EM) is a leading technology to resolve the structure of molecules. Early in the process, the user detects potential particle images in the raw data. Typically, there are many fa...")
• 19:43, 23 December 2024 WikiSysop talk contribs created page 2024Jamali Modelangelo (Created page with "== Citation == K. Jamali, L. Käll, R. Zhang, A. Brown, D. Kimanius, and S. H. Scheres, “Automated model building and protein identification in cryo-EM maps,” Nature, vol. 628, no. 8007, pp. 450–457, 2024. == Abstract == Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention in three-dimensional computer graphics programs1,2. Here we present ModelAngelo, a machine-learnin...")
• 19:34, 23 December 2024 WikiSysop talk contribs created page 2023Beton Fitting (Created page with "== Citation == J. G. Beton, T. Cragnolini, M. Kaleel, T. Mulvaney, A. Sweeney, and M. Topf, “Integrating model simulation tools and cryo-electron microscopy,” Wiley Interdisciplinary Reviews: Computational Molecular Science, vol. 13, no. 3, p. e1642, 2023. == Abstract == The power of computer simulations, including machine-learning, has become an inseparable part of scientific analysis of biological data. This has significantly impacted the field of cryogenic elec...")
• 19:27, 23 December 2024 WikiSysop talk contribs created page 2023Geva AbInitio (Created page with "== Citation == A. S. Geva and Y. Shkolnisky, “A common lines approach for ab initio modeling of molecules with tetrahedral and octahedral symmetry,” SIAM J. on Imaging Sciences, vol. 16, no. 4, pp. 1978–2014, 2023. == Abstract == A main task in cryo-electron microscopy single particle reconstruction is to nd a three-dimensional model of a molecule given a set of its randomly oriented and positioned noisy projection-images. In this work, we propose an algorithm f...")
• 08:16, 19 December 2024 WikiSysop talk contribs created page 2023Harpaz Alignment (Created page with "== Citation == Y. Harpaz and Y. Shkolnisky, “Three-dimensional alignment of density maps in cryo-electron microscopy,” Biological Imaging, vol. 3, p. e8, 2023. == Abstract == A common task in cryo-electron microscopy data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for aligning three-dimensional density maps, which exploits common lines between projection images of the maps. The algorithm is ful...")
• 08:02, 19 December 2024 WikiSysop talk contribs created page 2022Bharadwaj Scattering (Created page with "== Citation == A. Bharadwaj and A. J. Jakobi, “Electron scattering properties of biological macromolecules and their use for cryo-EM map sharpening,” Faraday Discussions, vol. 240, pp. 168–183, 2022. == Abstract == Resolution-dependent loss of contrast in cryo-EM maps may obscure features at high resolution that are critical for map interpretation. Post-processing of cryo-EM maps can improve the interpretability by adjusting the resolution-dependence of structur...")
• 10:46, 12 December 2024 Bzuber talk contribs created page 2024Khosrozadeh CryoVesNet (created the page)
• 08:40, 12 December 2024 WikiSysop talk contribs created page 2024Karimi Vesicle (Created page with "== Citation == R. Karimi, C. E. Coupland, and J. L. Rubinstein, “Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles,” J. Structural Biology, vol. 216, no. 4, p. 108148, 2024. == Abstract == Electron cryomicroscopy (cryo-EM) has recently allowed determination of near-atomic resolution structures of membrane proteins and protein complexes embedded in lipid vesicles. However, particle selection from electron micrographs of t...")
• 08:35, 12 December 2024 WikiSysop talk contribs created page 2024Remis Damage (Created page with "== Citation == J. Remis et al., “Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage,” Journal of Structural Biology, p. 108150, 2024. == Abstract == Apoferritin (apoF) is commonly used as a test specimen in single-particle electron cryo-microscopy (cryo-EM), since it consistently produces density maps that go to 3 Å resolution or higher. When we imaged apoF with a laser phase plate (LPP), however, we observed more severe particle-to-p...")
• 08:30, 12 December 2024 WikiSysop talk contribs created page 2024Hsieh MinIce (Created page with "== Citation == C.-C. Hsieh, Z.-J. Lin, and L.-J. Lai, “Minimizing ice contamination during specimen preparation for cryo-soft X-ray tomography and cryo-electron tomography,” Journal of Structural Biology: X, vol. 10, p. 100113, 2024. == Abstract == Cryo-soft X-ray tomography (cryo-SXT) is a newly developed technique for imaging 3D whole cells in nearly native states. Cryo-SXT users require the preparation of numerous cryo-sample grids to use the allocated beamtime...")
• 08:04, 12 December 2024 WikiSysop talk contribs created page 2024Schiotz Review (Created page with "== Citation == O. H. Schiøtz, S. Klumpe, J. M. Plitzko, and C. J. Kaiser, “Cryo-electron tomography: en route to the molecular anatomy of organisms and tissues,” Biochemical Society Transactions, p. BST20240173, 2024. == Abstract == Cryo-electron tomography (cryo-ET) has become a key technique for obtaining structures of macromolecular complexes in their native environment, assessing their local organization and describing the molecular sociology of the cell. Whi...")
• 06:34, 12 December 2024 WikiSysop talk contribs created page 2024Harley 40 (Created page with "== Citation == I. Harley, F. Mazzotta, X. Shaulli, F. Scheffold, K. Landfester, and I. Lieberwirth, “Practical considerations for plunge freezing samples over 40° C for Cryo-EM,” Micron, p. 103745, 2024. == Abstract == Cryo-EM is now an established tool for examining samples in their native, hydrated states—a leap made possible by vitrification. Utilising this sample preparation method to directly visualise temperature-responsive samples allows for deeper insig...")
• 15:07, 18 November 2024 WikiSysop talk contribs created page 2024deLaRosa EMHub (Created page with "== Citation == J. M. de la Rosa-Trevin et al., “EMhub: a web platform for data management and on-the-fly processing in scientific facilities,” Biological Crystallography, vol. 80, no. 11, 2024. == Abstract == Most scientific facilities produce large amounts of heterogeneous data at a rapid pace. Managing users, instruments, reports and invoices presents additional challenges. To address these challenges, EMhub, a web platform designed to support the daily operatio...")
• 09:26, 12 November 2024 Garygangren talk contribs created page 2015Zhang IgG1 (Created page with "== Citation == 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography. X. Zhang, L. Zhang, H. Tong, B. Peng, M.J. Rames, S. Zhang, G. Ren. Scientific Reports, (2015) , 5, 09803; doi: 10.1038/srep09803 == Abstract == Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these metho...")
• 09:24, 12 November 2024 Garygangren talk contribs created page 2016Zhang DNANG (Created page with "== Citation == Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography, Meng Zhang, César Díaz-Celis, Bibiana Onoa, Cristhian Cañari-Chumpitaz, Katherinne I. Requejo, Jianfang Liu, Michael Vien, Eva Nogales, Gang Ren, and Carlos Bustamante, Molecular Cell, (2022), 18;82(16):3000-3014.e9; PMID: 35907400 DOI: 10.1016/j.molcel.2022.06.032 == Abstract == It has been proposed that the intrinsic property of nucleosom...")
• 09:23, 12 November 2024 Garygangren talk contribs created page 2018Lei DNABennet (Created page with "== Citation == Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography, Meng Zhang, César Díaz-Celis, Bibiana Onoa, Cristhian Cañari-Chumpitaz, Katherinne I. Requejo, Jianfang Liu, Michael Vien, Eva Nogales, Gang Ren, and Carlos Bustamante, Molecular Cell, (2022), 18;82(16):3000-3014.e9; PMID: 35907400 DOI: 10.1016/j.molcel.2022.06.032 == Abstract == It has been proposed that the intrinsic property of nucleosom...")
• 09:22, 12 November 2024 Garygangren talk contribs created page 2022Zhang NucleosomeTrasition (Created page with "== Citation == Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography, Meng Zhang, César Díaz-Celis, Bibiana Onoa, Cristhian Cañari-Chumpitaz, Katherinne I. Requejo, Jianfang Liu, Michael Vien, Eva Nogales, Gang Ren, and Carlos Bustamante, Molecular Cell, (2022), 18;82(16):3000-3014.e9; PMID: 35907400 DOI: 10.1016/j.molcel.2022.06.032 == Abstract == It has been proposed that the intrinsic property of nucleosom...")
• 09:16, 12 November 2024 Garygangren talk contribs created page 2024Zhang Nucleosome (Created page with "== Citation == Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography, Meng Zhang, César Díaz-Celis, Jianfang Liu, Jinhui Tao, Paul D. Ashby, Carlos Bustamante, Gang Ren, Nature Comm., (2024), 15, 4395. doi:10.1038/s41467-024-48305-1 == Abstract == The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural de...")
• 09:15, 12 November 2024 Garygangren talk contribs created page 2024Liu RNA (Created page with "== Citation == Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography, Jianfang Liu, Ewan K.S. McRae, Meng Zhang, Cody Geary, Ebbe Sloth Andersen, Gang Ren, Nature Comm., (2024), 15, 9084. doi: 10.1038/s41467-024-52914- == Abstract == Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs betw...")
• 09:10, 12 November 2024 Garygangren talk contribs created page 2016Liu AutoET (Created page with "== Citation == Fully Mechanically Controlled Automated Electron Microscopic Tomography , Jinxin Liu, Hongchang Li, Lei Zhang, Matthew Rames, Meng Zhang, Yadong Yu, Bo Peng, César Díaz Celis, April Xu, Qin Zou, Xu Yang, Xuefeng Chen, Gang Ren, Scientific Reports, (2016), 6:29231, doi: 10.1038/srep29231 == Abstract == Knowledge of three-dimensional (3D) structures of each individual particles of asymmetric and flexible proteins is essential in understanding those protei...")
• 09:08, 12 November 2024 Garygangren talk contribs created page 2016Liu Aquasition (Created page with "== Citation == Fully Mechanically Controlled Automated Electron Microscopic Tomography , Jinxin Liu, Hongchang Li, Lei Zhang, Matthew Rames, Meng Zhang, Yadong Yu, Bo Peng, César Díaz Celis, April Xu, Qin Zou, Xu Yang, Xuefeng Chen, Gang Ren, Scientific Reports, (2016), 6:29231, doi: 10.1038/srep29231 == Abstract == Knowledge of three-dimensional (3D) structures of each individual particles of asymmetric and flexible proteins is essential in understanding those protei...")
• 09:05, 12 November 2024 Garygangren talk contribs created page 2018Wu Contrast (Created page with "== Citation == An Algorithm for Enhancing the Image Contrast of Electron Tomography, Hao Wu, Xiaobo Zhai, Dongsheng Lei, Jianfang Liu, Yadong Yu, Rongfang Bie, Gang Ren, Scientific Reports., (2018), 8(1):16711, PMID: 30420636 == Abstract == Three-dimensional (3D) reconstruction of a single protein molecule is essential for understanding the relationship between the structural dynamics and functions of the protein. Electron tomography (ET) provides a tool for imaging an...")
• 08:59, 12 November 2024 Garygangren talk contribs created page 2020Zhai LoTToR (Created page with "== Citation == LoTToR: An Algorithm for Missing-Wedge Correction of the Low-Tilt Tomographic 3D Reconstruction of a Single-Molecule Structure, Xiaobo Zhai, Dongsheng Lei, Meng Zhang, Jianfang Liu, Hao Wu, Yadong Yu, Lei Zhang, Gang Ren, Scientific Reports, (2020), 10, 10489. Doi: 10.1038/s41598-020-66793-1 == Abstract == A single-molecule three-dimensional (3D) structure is essential for understanding the thermal vibrations and dynamics as well as the conformational cha...")
• 08:51, 12 November 2024 Garygangren talk contribs created page 2012Zhang IPET (Created page with "== Citation == Zhang L, Ren G (2012) IPET and FETR: Experimental Approach for Studying Molecular Structure Dynamics by Cryo-Electron Tomography of a Single-Molecule Structure. PLoS ONE 7(1): e30249 == Abstract == The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle re...")
• 08:48, 12 November 2024 Garygangren talk contribs created page 2022Han Radiation (Created page with "== Citation == Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination, Han Xue, Meng Zhang, Jianfang Liu, Jianjun Wang, Gang Ren, Frontier in Chemistry, (2022), 10:889203. DOI: 10.3389/fchem.2022.889203 == Abstract == To understand the dynamic structure–function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in...")
• 08:45, 12 November 2024 Garygangren talk contribs created page 2023Kong ViralEntry (Created page with "== Citation == Facile hermetic TEM grid preparation for molecular imaging of hydrated biological samples at room temperature, Lingli Kong, Jianfang Liu, Meng Zhang, Zhuoyang Lu, Han Xue, Amy Ren, Jiankang Liu, Jinping Li, Wai Li Ling, Gang Ren, Nature Comm., (2023), 14, 5641. doi: 10.1038/s41467-023-41266-x == Abstract == The dynamics and structure of the liquid and vapor interface has remained elusive for decades due to the lack of an effective tool for directly visual...")
• 08:00, 12 November 2024 Garygangren talk contribs created page 2023Ren NucleosomeTrasition (Created page with "== Citation == Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography, Meng Zhang, César Díaz-Celis, Bibiana Onoa, Cristhian Cañari-Chumpitaz, Katherinne I. Requejo, Jianfang Liu, Michael Vien, Eva Nogales, Gang Ren, and Carlos Bustamante, Molecular Cell, (2022), 18;82(16):3000-3014.e9; PMID: 35907400 DOI: 10.1016/j.molcel.2022.06.032 == Abstract == It has been proposed that the intrinsic property of nucleosom...")
• 07:56, 12 November 2024 Garygangren talk contribs created page 2024Ren Nucleosome (Created page with "== Citation == Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography, Meng Zhang, César Díaz-Celis, Jianfang Liu, Jinhui Tao, Paul D. Ashby, Carlos Bustamante, Gang Ren, Nature Comm., (2024), 15, 4395. doi:10.1038/s41467-024-48305-1 == Abstract == The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural de...")
• 07:45, 12 November 2024 Garygangren talk contribs created page 2024Ren RNA (Created page with "== Citation == Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography, Jianfang Liu, Ewan K.S. McRae, Meng Zhang, Cody Geary, Ebbe Sloth Andersen, Gang Ren, Nature Comm., (2024), 15, 9084. doi: 10.1038/s41467-024-52914- == Abstract == Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs betw...")
• 12:19, 8 November 2024 Amartinez talk contribs created page 2014Martinez-Sanchez TomoSegMemTV (Created page with "== Citation == Martinez-Sanchez, A., Garcia, I., Asano, S., Lucic, V., & Fernandez, J. J. (2014). Robust membrane detection based on tensor voting for electron tomography. Journal of structural biology, 186(1), 49-61. == Abstract == Electron tomography enables three-dimensional (3D) visualization and analysis of the subcellular architecture at a resolution of a few nanometers. Segmentation of structural components present in 3D images (tomograms) is often necessary fo...")