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).

• 05:54, 21 August 2024 WikiSysop talk contribs created page 2024Klindt Disentanglement (Created page with "== Citation == Klindt, David A. / Hyvärinen, Aapo / Levy, Axel / Miolane, Nina / Poitevin, Frédéric. Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations. 2024. Frontiers in Molecular Biosciences, Vol. 11, p. 1393564 == Abstract == Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy...")
• 06:40, 20 August 2024 WikiSysop talk contribs created page 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...")
• 06:25, 20 August 2024 WikiSysop talk contribs created page 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...")
• 06:20, 20 August 2024 WikiSysop talk contribs created page 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...")
• 06:07, 20 August 2024 WikiSysop talk contribs created page 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...")
• 06:26, 19 August 2024 WikiSysop talk contribs created page 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...")
• 06:16, 16 August 2024 WikiSysop talk contribs created page 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...")
• 06:06, 16 August 2024 WikiSysop talk contribs created page 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...")
• 05:56, 16 August 2024 WikiSysop talk contribs created page 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...")
• 05:51, 16 August 2024 WikiSysop talk contribs created page 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...")
• 06:31, 14 August 2024 WikiSysop talk contribs created page 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...")
• 06:26, 14 August 2024 WikiSysop talk contribs created page 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...")
• 06:19, 14 August 2024 WikiSysop talk contribs created page 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...")
• 05:58, 14 August 2024 WikiSysop talk contribs created page 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...")
• 05:47, 14 August 2024 WikiSysop talk contribs created page 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...")
• 06:50, 13 August 2024 WikiSysop talk contribs created page 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...")
• 06:35, 13 August 2024 WikiSysop talk contribs created page 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...")
• 06:28, 13 August 2024 WikiSysop talk contribs created page 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...")
• 06:23, 13 August 2024 WikiSysop talk contribs created page 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...")
• 07:14, 12 August 2024 WikiSysop talk contribs created page 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...")
• 07:03, 12 August 2024 WikiSysop talk contribs created page 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...")
• 06:56, 12 August 2024 WikiSysop talk contribs created page 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...")
• 06:24, 12 August 2024 WikiSysop talk contribs created page 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...")
• 06:16, 12 August 2024 WikiSysop talk contribs created page 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...")
• 06:11, 12 August 2024 WikiSysop talk contribs created page 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...")
• 06:43, 9 August 2024 WikiSysop talk contribs created page 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...")
• 06:32, 9 August 2024 WikiSysop talk contribs created page 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...")
• 06:24, 9 August 2024 WikiSysop talk contribs created page 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...")
• 06:15, 9 August 2024 WikiSysop talk contribs created page 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...")
• 06:09, 9 August 2024 WikiSysop talk contribs created page 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...")
• 05:48, 9 August 2024 WikiSysop talk contribs created page 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...")
• 15:48, 8 August 2024 WikiSysop talk contribs created page 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...")
• 15:33, 8 August 2024 WikiSysop talk contribs created page 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...")
• 06:35, 8 August 2024 WikiSysop talk contribs created page 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...")
• 06:18, 8 August 2024 WikiSysop talk contribs created page 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...")
• 06:10, 8 August 2024 WikiSysop talk contribs created page 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...")
• 06:06, 8 August 2024 WikiSysop talk contribs created page 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...")
• 06:02, 8 August 2024 WikiSysop talk contribs created page 2024Amisaki Multilevel (Created page with "== Citation == Amisaki, Takashi. Multilevel superposition for deciphering the conformational variability of protein ensembles. 2024. Briefings in Bioinformatics, Vol. 25, No. 3, p. bbae137 == Abstract == The dynamics and variability of protein conformations are directly linked to their functions.Many comparative studies of X-ray protein structures have been conducted to elucidate the relevant conformational changes, dynamics and heterogeneity. The rapid increase in th...")
• 05:54, 8 August 2024 WikiSysop talk contribs created page 2024Titarenko optimal (Created page with "== Citation == Titarenko, Valeriy / Roseman, Alan M. Optimal 3D angular sampling with applications to cryo-EM problems. 2024. Journal of Structural Biology, Vol. 216, No. 2, p. 108083 == Abstract == The goal of cryo-EM experiments in the biological sciences is to determine the atomic structure of a molecule and deduce insights into its functions and mechanisms. Despite improvements in instrumentation for data collection and new software algorithms, in most cases, indi...")
• 05:41, 8 August 2024 WikiSysop talk contribs created page 2024Muller Common (Created page with "== Citation == Muller, Tommi / Duncan, Adriana L. / Verbeke, Eric / Kileel, Joe. Algebraic Constraints and Algorithms for Common Lines in Cryo-EM. 2024. Biological Imaging, p. 1-30 == Abstract == We revisit the topic of common lines between projection images in single particle cryo-electron microscopy (cryo- EM). We derive a novel low-rank constraint on a certain 2nxn matrix storing properly-scaled basis vectors for the common lines between n projection images of one...")
• 08:11, 7 August 2024 WikiSysop talk contribs created page 2024Mueller Facility (Created page with "== Citation == Mueller-Dieckmann, Christoph / Grinzato, Alessandro / Effantin, Grégory / Fenel, Daphna / Flot, David / Schoehn, Guy / Leonard, Gordon / Kandiah, Eaazhisai. From solution to structure: empowering inclusive cryo-EM with a pre-characterization pipeline for biological samples. 2024. J. Applied Crystallography, Vol. 57, No. 2 == Abstract == In addressing the challenges faced by laboratories and universities with limited (or no) cryo-electron microscopy (cr...")
• 06:52, 7 August 2024 WikiSysop talk contribs created page 2024Powell TomoDRGN (Created page with "== Citation == Powell, Barrett M. / Davis, Joseph H. Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN. 2024. Nature Methods, p. 1-12 == Abstract == Cryo-electron tomography (cryo-ET) enables observation of macromolecular complexes in their native, spatially contextualized cellular environment. Cryo-ET processing software to visualize such complexes at nanometer resolution via iterative alignment and averaging are well developed but rely...")
• 06:42, 7 August 2024 WikiSysop talk contribs created page 2024Shi Priors (Created page with "== Citation == Shi, Bin / Zhang, Kevin / Fleet, David J. / McLeod, Robert A. / Miller, R.J. Dwayne / Howe, Jane Y. Deep generative priors for biomolecular 3D heterogeneous reconstruction from cryo-EM projections. 2024. J. Structural Biology, Vol. 216, No. 2, p. 108073 == Abstract == Cryo-electron microscopy has become a powerful tool to determine three-dimensional (3D) structures of rigid biological macromolecules from noisy micrographs with single-particle reconstruc...")
• 06:24, 7 August 2024 WikiSysop talk contribs created page 2022Vilela Feret (Created page with "== Citation == Vilela, Fernando / Bezault, Armel / de Francisco, Borja Rodriguez / Sauvanet, Cécile / Xu, Xiao-Ping / Swift, Mark F. / Yao, Yong / Marrasi, Francesca M. / Hanein, Dorit / Volkmann, Niels. Characterization of heterogeneity in nanodisc samples using Feret signatures. 2022. J. Structural Biology, Vol. 214, No. 4, p. 107916 == Abstract == Nanodiscs have become a popular tool in structure determination of membrane proteins using cryogenic electron microsco...")
• 06:18, 7 August 2024 WikiSysop talk contribs created page 2024Nottelet Feret (Created page with "== Citation == Nottelet, Pierre / Van Blerkom, Peter / Xu, Xiao-Ping / Hanein, Dorit / Volkmann, Niels. CryoEM Workflow Acceleration with Feret Signatures. 2024. Intl. J. Molecular Sciences, Vol. 25, No. 14, p. 7593 == Abstract == Common challenges in cryogenic electron microscopy, such as orientation bias, conformational diversity, and 3D misclassification, complicate single particle analysis and lead to significant resource expenditure. We previously introduced an i...")
• 06:15, 7 August 2024 WikiSysop talk contribs created page 2022Rodriguez Mepsi (Created page with "== Citation == Rodríguez de Francisco, Borja / Bezault, Armel / Xu, Xiao-Ping / Hanein, Dorit / Volkmann, Niels. MEPSi: A tool for simulating tomograms of membrane-embedded proteins. 2022. J. Structural Biology, Vol. 214, No. 4, p. 107921 == Abstract == The throughput and fidelity of cryogenic cellular electron tomography (cryo-ET) is constantly increasing through advances in cryogenic electron microscope hardware, direct electron detection devices, and powerful ima...")
• 05:50, 7 August 2024 WikiSysop talk contribs created page 2024vanBlerkom GoldX (Created page with "== Citation == Van Blerkom, Peter / Bezault, Armel / Sauvanet, Cécile / Hanein, Dorit / Volkmann, Niels. The GoldX Fiducial Eraser. 2024. Intl. J. Molecular Sciences, Vol. 25, No. 13 == Abstract == Gold nanoparticles with sizes in the range of 5–15 nm are a standard method of providing fiducial markers to assist with alignment during reconstruction in cryogenic electron tomography. However, due to their high electron density and resulting contrast when compared to...")
• 07:01, 6 August 2024 WikiSysop talk contribs created page 2024Huang Joint (Created page with "== Citation == Huang, Qinwen / Zhou, Ye / Liu, Hsuan-Fu / Bartesaghi, Alberto. Joint micrograph denoising and protein localization in cryo-electron microscopy. 2024. Biological Imaging, Vol. 4 == Abstract == Cryo-electron microscopy (cryo-EM) is an imaging technique that allows the visualization of proteins and macromolecular complexes at near-atomic resolution. The low electron-doses used to prevent radiation damage to the biological samples, result in images where t...")
• 06:54, 6 August 2024 WikiSysop talk contribs created page 2024wwPDB EMDB (Created page with "== Citation == The PDB consortium, EMDB—the electron microscopy data bank, 2024, Nucleic acids research, Vol. 52, No. D1, p. D456-D465 == Abstract == The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by the Worldwide Protein Data Bank consortium (wwPDB; wwpdb.org) as a wwPDB Core Archi...")
• 06:43, 6 August 2024 WikiSysop talk contribs created page 2024Chung CryoForum (Created page with "== Citation == Chung, Szu-Chi. Cryo-forum: A framework for orientation recovery with uncertainty measure with the application in cryo-EM image analysis. 2024. J. Structural Biology, Vol. 216, No. 1, p. 108058 == Abstract == In single-particle cryo-electron microscopy (cryo-EM), efficient determination of orientation parameters for particle images poses a significant challenge yet is crucial for reconstructing 3D structures. This task is complicated by the high noise l...")