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20 August 2024
- 06:4006:40, 20 August 2024 diff hist +1,645 N 2024Aiyer Workflow Created page with "== Citation == Aiyer, Sriram / Baldwin, Philip R. / Tan, Shi Min / Shan, Zelin / Oh, Juntaek / Mehrani, Atousa / Bowman, Marianne E. / Louie, Gordon / Passos, Dario Oliveira / Đorđević-Marquardt, Selena / others. Overcoming resolution attenuation during tilted cryo-EM data collection. 2024. Nature communications, Vol. 15, No. 1, p. 389 == Abstract == Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting “prefe..." current
- 06:3906:39, 20 August 2024 diff hist +90 Main Page →3D Reconstruction
- 06:2506:25, 20 August 2024 diff hist +1,508 N 2024Coray Automated Created page with "== Citation == Coray, Raffaele / Navarro, Paula / Scaramuzza, Stefano / Stahlberg, Henning / Castaño-Diez, Daniel, Automated fiducial-based alignment of cryo-electron tomography tilt series in Dynamo, 2024, Structure, Vol. 32, p. 1-12 == Abstract == With the advent of modern technologies for cryo-electron tomography (cryo-ET), high-quality tilt series are more rapidly acquired than processed and analyzed. Thus, a robust and fast-automated alignment for batch processi..." current
- 06:2506:25, 20 August 2024 diff hist +98 Main Page →Image alignment
- 06:2006:20, 20 August 2024 diff hist +1,666 N 2024Read Interactive Created page with "== Citation == Read, Randy J. / Pettersen, Eric F. / McCoy, Airlie J. / Croll, Tristan I. / Terwilliger, Thomas C. / Poon, Billy K. / Meng, Elaine C. / Liebschner, Dorothee / Adams, Paul D. Likelihood-based interactive local docking into cryo-EM maps in ChimeraX. 2024. Acta Crystallographica Section D, Vol. 80, p. 588-598 == Abstract == The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particular..." current
- 06:1906:19, 20 August 2024 diff hist +68 Main Page →Fitting and docking
- 06:0706:07, 20 August 2024 diff hist +1,523 N 2024Zhu SIRM Created page with "== Citation == Zhu, Dongjie / Cao, Weili / Li, Junxi / Wu, Chunling / Cao, Duanfang / Zhang, Xinzheng. Correction of preferred orientation--induced distortion in cryo-electron microscopy maps. 2024. Science Advances, Vol. 10, No. 30, p. eadn0092 == Abstract == Reconstruction maps of cryo–electron microscopy (cryo-EM) exhibit distortion when the cryo-EM dataset is incomplete, usually caused by unevenly distributed orientations. Prior efforts had been attempted to ad..." current
- 06:0606:06, 20 August 2024 diff hist +102 Main Page →3D Reconstruction
19 August 2024
- 06:2606:26, 19 August 2024 diff hist +1,516 N 2024Rangan CryoDRGNET Created page with "== Citation == Rangan, Ramya / Feathers, Ryan / Khavnekar, Sagar / Lerer, Adam / Johnston, Jake D. / Kelley, Ron / Obr, Martin / Kotecha, Abhay / Zhong, Ellen D. CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells. 2024. Nature Methods, p. 1-9 == Abstract == Advances in cryo-electron tomography (cryo-ET) have produced new opportunities to visualize the structures of dynamic macromolecules in native cellular environmen..." current
- 06:2506:25, 19 August 2024 diff hist +95 Main Page →Subtomogram analysis
16 August 2024
- 06:1606:16, 16 August 2024 diff hist +1,311 N 2024Liu Graphene Created page with "== Citation == Liu, Nan / Wang, Hong-Wei. Graphene in cryo-EM specimen optimization. 2024. Current Opinion in Structural Biology, Vol. 86, p. 102823 == Abstract == Specimen preparation is a critical but challenging step in highresolution cryogenic electron microscopy (cryo-EM) structural analysis of macromolecules. In the past decade, graphene has gained much recognition as the supporting substrate to optimize cryo-EM specimen preparation. It improves macromolecule em..." current
- 06:1506:15, 16 August 2024 diff hist +88 Main Page →Sample preparation
- 06:0606:06, 16 August 2024 diff hist +1,239 N 2024Hutchings Review Created page with "== Citation == Hutchings, Joshua / Villa, Elizabeth. Expanding insights from in situ cryo-EM. 2024. Current Opinion in Structural Biology, Vol. 88, p. 102885 == Abstract == The combination of cryo-electron tomography and subtomogram analysis affords 3D high-resolution views of biological macromolecules in their native cellular environment, or in situ. Streamlined methods for acquiring and processing these data are advancing attainable resolutions into the realm of dru..." current
- 06:0506:05, 16 August 2024 diff hist +80 Main Page →Books and reviews
- 05:5605:56, 16 August 2024 diff hist +1,697 N 2024Maurer PyTME Created page with "== Citation == Maurer, Valentin J. / Siggel, Marc / Kosinski, Jan. PyTME (Python Template Matching Engine): A fast, flexible, and multi-purpose template matching library for cryogenic electron microscopy data. 2024. SoftwareX, Vol. 25, p. 101636 == Abstract == Cryogenic electron microscopy (cryo-EM) is a key method in structural and cell biology. Analysis of cryo-EM images requires interpretation of noisy, low-resolution densities, which relies on identifying the most..." current
- 05:5405:54, 16 August 2024 diff hist +74 Main Page →Software
- 05:5105:51, 16 August 2024 diff hist +1,708 N 2024Song RMSFNet Created page with "== Citation == Song, Xintao / Bao, Lei / Feng, Chenjie / Huang, Qiang / Zhang, Fa / Gao, Xin / Han, Renmin. Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information. 2024. Nature Communications, Vol. 15, No. 1, p. 5538 == Abstract == The dynamics of proteins are crucial for understanding their mechanisms. However, computationally predicting protein dynamic information has proven chal..." current
- 05:5005:50, 16 August 2024 diff hist +105 Main Page →3D Heterogeneity
14 August 2024
- 06:3106:31, 14 August 2024 diff hist +1,083 N 2024Bock MD Created page with "== Citation == Bock, Lars V. / Igaev, Maxim / Grubmüller, Helmut. Single-particle Cryo-EM and molecular dynamics simulations: A perfect match. 2024. Current Opinion in Structural Biology, Vol. 86, p. 102825 == Abstract == Knowledge of the structure and dynamics of biomolecules is key to understanding the mechanisms underlying their biological functions. Single-particle cryo-electron microscopy (cryo-EM) is a powerful structural biology technique to characterize compl..." current
- 06:3006:30, 14 August 2024 diff hist +89 Main Page →Books and reviews
- 06:2606:26, 14 August 2024 diff hist +1,388 N 2024Kimanius Heterogeneity Created page with "== Citation == Kimanius, Dari / Schwab, Johannes. Confronting heterogeneity in cryogenic electron microscopy data: Innovative strategies and future perspectives with data-driven methods. 2024. Current Opinion in Structural Biology, Vol. 86, p. 102815 == Abstract == The surge in the influx of data from cryogenic electron microscopy (cryo-EM) experiments has intensified the demand for robust algorithms capable of autonomously managing structurally heterogeneous dataset..." current
- 06:2506:25, 14 August 2024 diff hist +80 Main Page →Books and reviews
- 06:1906:19, 14 August 2024 diff hist +1,363 N 2024Cheng Automated Created page with "== Citation == Cheng, Anchi / Yu, Yue. Recent advances in data collection for Cryo-EM methods. 2024. Current Opinion in Structural Biology, Vol. 86, p. 102795 == Abstract == Methods of transmission electron microscopy (TEM) are typically used to resolve structures of vitrified biological specimens using both single particle analysis (SPA) and tomographic methods and use both conventional as well as scanning transmission modes of data collection. Automation of data col..." current
- 06:1806:18, 14 August 2024 diff hist +72 Main Page →Books and reviews
- 05:5805:58, 14 August 2024 diff hist +2,019 N 2024Wankowicz qFit Created page with "== Citation == Wankowicz, Stephanie A. / Ravikumar, Ashraya / Sharma, Shivani / Riley, Blake / Raju, Akshay / Hogan, Daniel W. / Flowers, Jessica / van den Bedem, Henry / Keedy, Daniel A. / Fraser, James S. Automated multiconformer model building for X-ray crystallography and cryo-EM. 2024. eLife, Vol. 12, p. RP90606 == Abstract == In their folded state, biomolecules exchange between multiple conformational states that are crucial for their function. Traditional struc..." current
- 05:5805:58, 14 August 2024 diff hist +79 Main Page →Fitting and docking
- 05:4705:47, 14 August 2024 diff hist +1,259 N 2024Giri CryoStruct Created page with "== Citation == Giri, Nabin / Cheng, Jianlin. De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM. 2024. Nature Communications, Vol. 15, No. 1, p. 5511 == Abstract == Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates..." current
- 05:4605:46, 14 August 2024 diff hist +85 Main Page →Fitting and docking
13 August 2024
- 06:5006:50, 13 August 2024 diff hist +1,575 N 2024Lytje SAXS Created page with "== Citation == Lytje, Kristian / Pedersen, Jan Skov. Validation of electron-microscopy maps using solution small-angle X-ray scattering. 2024. Acta Crystallographica Section D: Structural Biology, Vol. 80, No. 7, p. 493-505 == Abstract == The determination of the atomic resolution structure of biomacromolecules is essential for understanding details of their function. Traditionally, such a structure determination has been performed with crystallographic or nuclear res..." current
- 06:5006:50, 13 August 2024 diff hist +79 Main Page →Validation
- 06:3506:35, 13 August 2024 diff hist +1,113 N 2024Xu Miffi Created page with "== Citation == Xu, Da / Ando, Nozomi. Miffi: Improving the accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information. 2024. J. Structural Biology, Vol. 216, No. 2, p. 108072 == Abstract == Efficient and high-accuracy filtering of cryo-electron microscopy (cryo-EM) micrographs is an emerging challenge with the growing speed of data collection and sizes of datasets. Convolutional neural networks (CNNs) are machine learning models..." current
- 06:3406:34, 13 August 2024 diff hist +81 Main Page →Automated data collection
- 06:2906:29, 13 August 2024 diff hist +7 Main Page →Segmentation
- 06:2806:28, 13 August 2024 diff hist +1,641 N 2024Siggel ColabSeg Created page with "== Citation == Siggel, Marc / Jensen, Rasmus K. / Maurer, Valentin J. / Mahamid, Julia / Kosinski, Jan. ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data. 2024. J. Structural Biology, Vol. 216, No. 2, p. 108067 == Abstract == Cellular cryo-electron tomography (cryo-ET) has emerged as a key method to unravel the spatial and structural complexity of cells in their near-native state at unprecedented molecular..." current
- 06:2506:25, 13 August 2024 diff hist +81 Main Page →Segmentation
- 06:2306:23, 13 August 2024 diff hist +2,041 N 2024Jin Size Created page with "== Citation == Jin, Weisheng / Zhou, Ye / Bartesaghi, Alberto. Accurate size-based protein localization from cryo-ET tomograms. 2024. J. Structural Biology X, Vol. 10, p. 100104 == Abstract == Cryo-electron tomography (cryo-ET) combined with sub-tomogram averaging (STA) allows the determination of protein structures imaged within the native context of the cell at near-atomic resolution. Particle picking is an essential step in the cryo-ET/STA image analysis pipeline t..." current
- 06:2006:20, 13 August 2024 diff hist +67 Main Page →Subtomogram analysis
12 August 2024
- 07:1407:14, 12 August 2024 diff hist +1,606 N 2024Cruz Template Created page with "== Citation == Cruz-León, Sergio / Majtner, Tomáš / Hoffmann, Patrick / Kreysing, Jan P. / Tuijtel, Maarten W. / Schaefer, Stefan L. / Geißler, Katharina / Beck, Martin / Turoňová, Beata / Hummer, Gerhard. High-confidence 3D template matching for cryo-electron tomography. 2024. Biophysical Journal, Vol. 123, No. 3, p. 183a == Abstract == Visual proteomics attempts to build atlases of the molecular content of cells but the automated annotation of cryo electron to..." current
- 07:1307:13, 12 August 2024 diff hist +67 Main Page →Subtomogram analysis
- 07:0307:03, 12 August 2024 diff hist +599 N 2024Bowlby Flexible Created page with "== Citation == Bowlby, Beatrice. The dynamic duo: cryo-EM teams up with machine learning to visualize biomolecules in motion. 2024. Biotechniques, Vol. 76, p. 229-233 == Abstract == Cryo-EM has been a key technique in our understanding of biomolecular structures. Now, machine learning techniques are being used to put these structures in motion, revealing dynamic interactions and processes happening on a molecular and cellular level. == Keywords == == Links == https..." current
- 07:0207:02, 12 August 2024 diff hist +73 Main Page →Books and reviews
- 06:5606:56, 12 August 2024 diff hist +1,718 N 2024Sazzed CryoSSESeg Created page with "== Citation == Sazzed, Salim. Determining Protein Secondary Structures in Heterogeneous Medium-Resolution Cryo-EM Images Using CryoSSESeg. 2024. ACS Omega == Abstract == While the acquisition of cryo-electron microscopy (cryo-EM) at near-atomic resolution is becoming more prevalent, a considerable number of density maps are still resolved only at intermediate resolutions (5−10 Å). Due to the large variation in quality among these medium-resolution density maps, ext..." current
- 06:5506:55, 12 August 2024 diff hist +127 Main Page →Segmentation
- 06:2406:24, 12 August 2024 diff hist +1,399 N 2024Dahmani MDFF Created page with "== Citation == Dahmani, Zakaria L. / Scott, Ana Ligia / Vénien-Bryan, Catherine / Perahia, David / Costa, Mauricio G. S. MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search. 2024. J. Chemical Information and Modeling, Vol. 64, No. 13, p. 5151-5160 == Abstract == Molecular Dynamics Flexible Fitting (MDFF) is a widely used tool to refine high-resolution structures into cryo-EM density maps. Despit..." current
- 06:2306:23, 12 August 2024 diff hist +72 Main Page →Fitting and docking
- 06:1606:16, 12 August 2024 diff hist +1,262 N 2023Watson Review Created page with "== Citation == Watson, Abigail J. I. / Bartesaghi, Alberto. Advances in cryo-ET data processing: meeting the demands of visual proteomics. 2024. Current Opinion in Structural Biology, Vol. 87 p. 102861 == Abstract == Cryogenic electron tomography (cryo-ET), a method that enables the viewing of biomolecules in near-native environments at high resolution, is rising in accessibility and applicability. Over the past several years, once slow sample preparation and data col..." current
- 06:1506:15, 12 August 2024 diff hist +95 Main Page →Books and reviews
- 06:1106:11, 12 August 2024 diff hist +1,611 N 2024Gillman Cone Created page with "== Citation == Gillman, Cody / Bu, Guanhong / Danelius, Emma / Hattne, Johan / Nannenga, Brent L. / Gonen, Tamir. Eliminating the missing cone challenge through innovative approaches. 2024. Journal of Structural Biology: X, Vol. 9, p. 100102 == Abstract == Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle arises with plat..." current
- 06:1006:10, 12 August 2024 diff hist +3 Main Page →Sample Preparation
- 06:1006:10, 12 August 2024 diff hist +65 Main Page →Sample Preparation