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  • 15:07, 18 November 2024 ‎2024deLaRosa EMHub (hist | edit) ‎[1,770 bytes] ‎WikiSysop (talk | contribs) (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 ‎2015Zhang IgG1 (hist | edit) ‎[1,805 bytes] ‎Garygangren (talk | contribs) (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 ‎2016Zhang DNANG (hist | edit) ‎[1,727 bytes] ‎Garygangren (talk | contribs) (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 ‎2018Lei DNABennet (hist | edit) ‎[1,691 bytes] ‎Garygangren (talk | contribs) (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 ‎2022Zhang NucleosomeTrasition (hist | edit) ‎[2,160 bytes] ‎Garygangren (talk | contribs) (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 ‎2024Zhang Nucleosome (hist | edit) ‎[2,280 bytes] ‎Garygangren (talk | contribs) (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 ‎2024Liu RNA (hist | edit) ‎[1,959 bytes] ‎Garygangren (talk | contribs) (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 ‎2016Liu AutoET (hist | edit) ‎[1,938 bytes] ‎Garygangren (talk | contribs) (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 ‎2016Liu Aquasition (hist | edit) ‎[1,938 bytes] ‎Garygangren (talk | contribs) (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 ‎2018Wu Contrast (hist | edit) ‎[2,094 bytes] ‎Garygangren (talk | contribs) (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 ‎2020Zhai LoTToR (hist | edit) ‎[2,202 bytes] ‎Garygangren (talk | contribs) (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 ‎2012Zhang IPET (hist | edit) ‎[3,500 bytes] ‎Garygangren (talk | contribs) (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 ‎2022Han Radiation (hist | edit) ‎[2,157 bytes] ‎Garygangren (talk | contribs) (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 ‎2023Kong ViralEntry (hist | edit) ‎[1,831 bytes] ‎Garygangren (talk | contribs) (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 ‎2023Ren NucleosomeTrasition (hist | edit) ‎[2,359 bytes] ‎Garygangren (talk | contribs) (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 ‎2024Ren Nucleosome (hist | edit) ‎[2,280 bytes] ‎Garygangren (talk | contribs) (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 ‎2024Ren RNA (hist | edit) ‎[1,959 bytes] ‎Garygangren (talk | contribs) (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 ‎2014Martinez-Sanchez TomoSegMemTV (hist | edit) ‎[1,888 bytes] ‎Amartinez (talk | contribs) (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...")
  • 12:13, 8 November 2024 ‎2020Martinez-Sanchez PySeg (hist | edit) ‎[1,566 bytes] ‎Amartinez (talk | contribs) (Created page with "== Citation == Martinez-Sanchez, A., Kochovski, Z., Laugks, U. et al. Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms. Nat Methods 17, 209–216 (2020). https://doi.org/10.1038/s41592-019-0675-5 == Abstract == With faithful sample preservation and direct imaging of fully hydrated biological material, cryo-electron tomography provides an accurate representation of molecular architecture of cells. However, detection and...")
  • 12:00, 8 November 2024 ‎2024Martinez-Sanchez PolNet (hist | edit) ‎[2,426 bytes] ‎Amartinez (talk | contribs) (Python package for generating synthetic datasets of the cellular context for Cryo-Electron Tomography.)
  • 10:31, 8 November 2024 ‎2024Cameron REPIC (hist | edit) ‎[1,532 bytes] ‎WikiSysop (talk | contribs) (Created page with "== Citation == C. J. Cameron, S. J. Seager, F. J. Sigworth, H. D. Tagare, and M. B. Gerstein, “REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers,” Communications Biology, vol. 7, no. 1, p. 1421, 2024. == Abstract == Cryo-EM particle identification from micrographs (“picking”) is challenging due to the low signal-to-noise ratio and lack of ground truth for particle locations. State-of-the-art computa...")
  • 10:28, 8 November 2024 ‎2024Li EM2NA (hist | edit) ‎[1,474 bytes] ‎WikiSysop (talk | contribs) (Created page with "== Citation == T. Li, H. Cao, J. He, and S.-Y. Huang, “Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps,” Nature Communications, vol. 15, no. 1, p. 9367, 2024. == Abstract == Cryo-electron microscopy (cryo-EM) is one of the most powerful experimental methods for macromolecular structure determination. However, accurate DNA/RNA structure modeling from cryo-EM maps is still challenging especially for protein-DNA/RNA or multi-chai...")
  • 10:22, 8 November 2024 ‎2024Ermel DataPortal (hist | edit) ‎[494 bytes] ‎WikiSysop (talk | contribs) (Created page with "== Citation == U. Ermel et al., “A data portal for providing standardized annotations for cryo-electron tomography,” Nature Methods, pp. 1–3, 2024. == Abstract == We present the cryoET Data Portal (https://cryoetdataportal. czscience.com/), containing annotated cryoET datasets in standardized formats, as a resource for the cryoET community == Keywords == == Links == https://www.nature.com/articles/s41592-024-02477-2 == Related software == == Related methods...")
  • 10:16, 8 November 2024 ‎2024Wang DiffModeller (hist | edit) ‎[1,220 bytes] ‎WikiSysop (talk | contribs) (Created page with "== Citation == X. Wang, H. Zhu, G. Terashi, M. Taluja, and D. Kihara, “DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model,” Nature Methods, pp. 1–11, 2024. == Abstract == Cryogenic electron microscopy (cryo-EM) has now been widely used for determining multichain protein complexes. However, modeling a large complex structure, such as those with more than ten chains, is challenging, particularly when the map resolution de...")
  • 10:11, 8 November 2024 ‎2024Anuk Auction (hist | edit) ‎[1,113 bytes] ‎WikiSysop (talk | contribs) (Created page with "== Citation == S. Anuk, T. Bendory, and A. Painsky, “Image detection using combinatorial auction,” IEEE Open J. Signal Processing, 2024. == Abstract == This paper studies the optimal solution of the classical problem of detecting the location of multiple image occurrences in a two-dimensional, noisy measurement. Assuming the image occurrences do not overlap, we formulate this task as a constrained maximum likelihood optimization problem.We show that the maximum li...")
  • 10:06, 8 November 2024 ‎2024Chen EModelX (hist | edit) ‎[1,856 bytes] ‎WikiSysop (talk | contribs) (Created page with "== Citation == S. Chen, S. Zhang, X. Fang, L. Lin, H. Zhao, and Y. Yang, “Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences,” Nature Communications, vol. 15, no. 1, p. 8808, 2024. == Abstract == Cryo-electron microscopy (cryo-EM) technique is widely used for protein structure determination. Current automatic cryo-EM protein complex modeling methods mostly rely on prior chain separation. However, chain separation...")
  • 10:00, 8 November 2024 ‎2024Moriya GoToCloud (hist | edit) ‎[1,468 bytes] ‎WikiSysop (talk | contribs) (Created page with "== Citation == T. Moriya, Y. Yamada, M. Yamamoto, and T. Senda, “GoToCloud optimization of cloud computing environment for accelerating cryo-EM structure-based drug design,” Communications Biology, vol. 7, no. 1, p. 1320, 2024. == Abstract == Cryogenic electron microscopy (Cryo-EM) is a widely used technique for visualizing the 3D structures of many drug design targets, including membrane proteins, at atomic resolution. However, the necessary throughput for struct...")
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