User contributions for WikiSysop

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

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

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

06:4306:43, 9 August 2024 diff hist +1,792 N 2024Suder Workflow Created page with "== Citation == Suder, Diana S. / Gonen, Shane. Mitigating the Blurring Effect of CryoEM Averaging on a Flexible and Highly Symmetric Protein Complex through Sub-Particle Reconstruction. 2024. Intl. J. Molecular Sciences, Vol. 25, No. 11, p. 5665 == Abstract == Many macromolecules are inherently flexible as a feature of their structure and function. During single-particle CryoEM processing, flexible protein regions can be detrimental to highresolution reconstruction a..." current
06:4206:42, 9 August 2024 diff hist +118 Main Page →3D Reconstruction
06:3206:32, 9 August 2024 diff hist −11 2024Urzhumtseva VUE No edit summary current
06:3206:32, 9 August 2024 diff hist +1,763 N 2024Urzhumtseva VUE Created page with "== Citation == Urzhumtseva, Ludmila / Barchet, Charles / Klaholz, Bruno P. / Urzhumtsev, Alexandre G. Program VUE: analysing distributions of cryo-EM projections using uniform spherical grids. 2024. J. Applied Crystallography, Vol. 57, p. 865-876 == Abstract == Three-dimensional cryo electron microscopy reconstructions are obtained by extracting information from a large number of projections of the object. These projections correspond to different ‘views’ or ‘or..."
06:3106:31, 9 August 2024 diff hist +85 Main Page →Software
06:2406:24, 9 August 2024 diff hist +1,499 N 2024Wan StopGap Created page with "== Citation == Wan, William / Khavnekar, Sagar / Wagner, Jonathan. STOPGAP: an open-source package for template matching, subtomogram alignment and classification. 2024. Acta Crystallographica Section D: Structural Biology, Vol. 80, No. 5 == Abstract == Cryo-electron tomography (cryo-ET) enables molecular-resolution 3D imaging of complex biological specimens such as viral particles, cellular sections and, in some cases, whole cells. This enables the structural charact..." current
06:2306:23, 9 August 2024 diff hist +96 Main Page →Subtomogram analysis
06:1506:15, 9 August 2024 diff hist +2,725 N 2024Gaifas Blik Created page with "== Citation == Gaifas, Lorenzo / Kirchner, Moritz A. / Timmins, Joanna / Gutsche, Irina. Blik is an extensible 3D visualisation tool for the annotation and analysis of cryo-electron tomography data. 2024. PLoS biology, Vol. 22, No. 4, p. e3002447 == Abstract == Powerful, workflow-agnostic and interactive visualisation is essential for the ad hoc, humanin- the-loop workflows typical of cryo-electron tomography (cryo-ET). While several tools exist for visualisation and..." current
06:1406:14, 9 August 2024 diff hist +90 Main Page →Software
06:0906:09, 9 August 2024 diff hist +2,122 N 2024Vallat IHMCIF Created page with "== Citation == Vallat, Brinda / Webb, Benjamin M. / Westbrook, John D. / Goddard, Thomas D. / Hanke, Christian A. / Graziadei, Andrea / Peisach, Ezra / Zalevsky, Arthur / Sagendorf, Jared / Tangmunarunkit, Hongsuda / others. IHMCIF: an extension of the PDBx/mmCIF data standard for integrative structure determination methods. 2024. J. Molecular Biology, p. 168546 == Abstract == IHMCIF ( github.com/ihmwg/IHMCIF ) is a data information framework that supports archiving a..." current
06:0806:08, 9 August 2024 diff hist +91 Main Page →Databases
05:4805:48, 9 August 2024 diff hist +1,229 N 2024Bochtler Probes Created page with "== Citation == Bochtler, Matthias. X-rays, electrons, and neutrons as probes of atomic matter. 2024. Structure, Vol. 32, p. 630-643 == Abstract == X-rays, electrons, and neutrons probe different properties of matter. X-rays feel electron density (ED). Electrons sense the electrostatic potential (ESP) of electrons and nuclei. Neutrons are sensitive to nuclear coherent scattering length (NCSL). While NCSL maps are widely understood to be different, ED and ESP maps are t..." current
05:4505:45, 9 August 2024 diff hist +100 Main Page →Image formation

15:4815:48, 8 August 2024 diff hist +1,424 N 2024Fan RL Created page with "== Citation == Fan, Quanfu / Li, Yilai / Yao, Yuguang / Cohn, John / Liu, Sijia / Xu, Ziping / Vos, Seychelle / Cianfrocco, Michael. Cryorl: Reinforcement learning enables efficient cryo-em data collection. 2024. Proc. IEEE/CVF Winter Conf. on Applications of Computer Vision. p. 7892-7902 == Abstract == Single-particle cryo-electron microscopy (cryo-EM) has become one of the mainstream structural biology techniques because of its ability to determine high-resolution s..." current
15:4715:47, 8 August 2024 diff hist +91 Main Page →Automated data collection
15:3315:33, 8 August 2024 diff hist +698 N 2020Maruthi Automatic Created page with "== Citation == Maruthi, Kashyap / Kopylov, Mykhailo / Carragher, Bridget. Automating decision making in the cryo-EM pre-processing pipeline. 2020. Structure, Vol. 28, No. 7. p. 727-729 == Abstract == In this issue of Structure, Li et al., 2020 describe machine learning methods that automate decision making in the cryo-EM pre-processing pipeline, eliminating the need for user-subjective decisions. They successfully tested this pipeline for a wide range of datasets, dem..." current
15:3115:31, 8 August 2024 diff hist +82 Main Page →Automated data collection
09:4909:49, 8 August 2024 diff hist −5 2024Henderikx Vitrojet No edit summary current
06:3506:35, 8 August 2024 diff hist +2,739 N 2024Fang Swin Created page with "== Citation == Fang, Kun / Wang, JinLing / Chen, QingFeng / Feng, Xian / Qu, YouMing / Shi, Jiachi / Xu, Zhuomin. Swin-cryoEM: Multi-class cryo-electron micrographs single particle mixed detection method. 2024. Plos one, Vol. 19, No. 4, p. e0298287 == Abstract == Cryo-electron micrograph images have various characteristics such as varying sizes, shapes, and distribution densities of individual particles, severe background noise, high levels of impurities, irregular sh..." current
06:3406:34, 8 August 2024 diff hist +64 Main Page →Automatic particle picking
06:1806:18, 8 August 2024 diff hist +1,822 N 2024Hatton EMinsight Created page with "== Citation == Hatton, Daniel / Cha, Jaehoon / Riggs, Stephen / Harrison, Peter J. / Thiyagalingam, Jeyan / Clare, Daniel K. / Morris, Kyle L. EMinsight: a tool to capture cryoEM microscope configuration and experimental outcomes for analysis and deposition. 2024. Acta Crystallographica Section D: Structural Biology, Vol. 80, No. 4, p. 259-269 == Abstract == The widespread adoption of cryoEM technologies for structural biology has pushed the discipline to new frontier..." current
06:1706:17, 8 August 2024 diff hist +157 Main Page →Automated data collection
06:1006:10, 8 August 2024 diff hist +2,116 N 2024Comet TomoLive Created page with "== Citation == Comet, Maxime / Dijkman, Patricia M. / Boer Iwema, Reint / Franke, Tilman / Masiulis, Simonas / Schampers, Ruud / Raschdorf, Oliver / Grollios, Fanis / Pryor, Edward E. / Drulyte, Ieva. Tomo Live: an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows. 2024. Biological Crystallography, Vol. 80, No. 4, p. 247-258 == Abstract == Data acquisition and processing for cryo-electron tomography can be a significant bo..." current
06:0906:09, 8 August 2024 diff hist +97 Main Page →Software
06:0606:06, 8 August 2024 diff hist +1,829 N 2024Henderikx Vitrojet Created page with "== Citation == Henderikx, Rene J. M. / Mann, Daniel / Domanska, Aušra / Dong, Jing / Shahzad, Saba / Lak, Behnam / Filopoulou, Aikaterini / Ludig, Damian / Grininger, Martin / Momoh, Jeffrey / others. VitroJet: new features and case studies. 2024. Biological Crystallography, Vol. 80, No. 4, p. 232-246 == Abstract == Single-particle cryo-electron microscopy has become a widely adopted method in structural biology due to many recent technological advances in microscope..."
06:0506:05, 8 August 2024 diff hist +65 Main Page →Sample preparation

User contributions for WikiSysop

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