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).

• 06:19, 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...")
• 06:26, 5 August 2024 WikiSysop talk contribs created page 2024Li EMRNA (Created page with "== Citation == Li, Tao / He, Jiahua / Cao, Hong / Zhang, Yi / Chen, Ji / Xiao, Yi / Huang, Sheng-You. All-atom RNA structure determination from cryo-EM maps. 2024. Nature Biotechnology, p. 1-9 == Abstract == Many methods exist for determining protein structures from cryogenic electron microscopy maps, but this remains challenging for RNA structures. Here we developed EMRNA, a method for accurate, automated determination of full-length all-atom RNA structures from cryo...")
• 06:04, 5 August 2024 WikiSysop talk contribs created page 2024Horstmann PATo (Created page with "== Citation == Horstmann, Anna / Riggs, Stephen / Chaban, Yuriy / Clare, Daniel K. / de Freitas, Guilherme / Farmer, David / Howe, Andrew / Morris, Kyle L. / Hatton, Daniel. A service-based approach to cryoEM facility processing pipelines at eBIC. 2024. Acta Crystallographica Section D: Structural Biology, Vol. 80, No. 3 == Abstract == Electron cryo-microscopy image-processing workflows are typically composed of elements that may, broadly speaking, be categorized as h...")
• 05:56, 5 August 2024 WikiSysop talk contribs created page 2024He SHOT (Created page with "== Citation == He, Bintao / Zhang, Fa / Feng, Chenjie / Yang, Jianyi / Gao, Xin / Han, Renmin. Accurate global and local 3D alignment of cryo-EM density maps using local spatial structural features. 2024. Nature Communications, Vol. 15, No. 1, p. 1593 == Abstract == Advances in cryo-electron microscopy (cryo-EM) imaging technologies have led to a rapidly increasing number of cryo-EM density maps. Alignment and comparison of density maps play a crucial role in interpre...")
• 05:44, 5 August 2024 WikiSysop talk contribs created page 2024Liu kinetic (Created page with "== Citation == Liu, Jiaxuan / Lu, Yonggang / Zhu, Li. A kinetic model for solving a combination optimization problem in ab-initio Cryo-EM 3D reconstruction. 2024. Briefings in Bioinformatics, Vol. 25, No. 2, p. bbad473 == Abstract == Cryo-Electron Microscopy (cryo-EM) is a widely used and effective method for determining the three-dimensional (3D) structure of biological molecules. For ab-initio Cryo-EM 3D reconstruction using single particle analysis (SPA), estimatin...")
• 06:12, 2 August 2024 WikiSysop talk contribs created page 2024Wang TomoNet (Created page with "== Citation == Wang, Hui / Liao, Shiqing / Yu, Xinye / Zhang, Jiayan / Zhou, Z. Hong. TomoNet: A streamlined cryogenic electron tomography software pipeline with automatic particle picking on flexible lattices. 2024. Biological Imaging, Vol. 4, p. e7 == Abstract == Cryogenic electron tomography (cryoET) is capable of determining in situ biological structures of molecular complexes at near-atomic resolution by averaging half a million subtomograms. While abundant compl...")
• 06:06, 2 August 2024 WikiSysop talk contribs created page 2023Matinyan TRPX (Created page with "== Citation == Matinyan, Senik / Abrahams, Jan Pieter. TERSE/PROLIX (TRPX)--a new algorithm for fast and lossless compression and decompression of diffraction and cryo-EM data. 2023. Acta Crystallographica Section A: Foundations and Advances, Vol. 79, No. 6 == Abstract == High-throughput data collection in crystallography poses significant challenges in handling massive amounts of data. Here, TERSE/PROLIX (or TRPX for short) is presented, a novel lossless compression...")
• 05:59, 2 August 2024 WikiSysop talk contribs created page 2024Kleywegt ArchivingValidation (Created page with "== Citation == Kleywegt, Gerard J. / Adams, Paul D. / Butcher, Sarah J. / Lawson, Catherine L. / Rohou, Alexis / Rosenthal, Peter B. / Subramaniam, Sriram / Topf, Maya / Abbott, Sanja / Baldwin, Philip R. / others. Community recommendations on cryoEM data archiving and validation. 2024. IUCrJ, Vol. 11, No. 2 == Abstract == In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures,...")
• 05:42, 2 August 2024 WikiSysop talk contribs created page 2019Urzhumtseva Review (Created page with "== Citation == Urzhumtseva, Ludmila / Urzhumtsev, Alexandre. py_convrot: rotation conventions, to understand and to apply. 2019. Journal of Applied Crystallography, Vol. 52, No. 4, p. 869-881 == Abstract == Rotation is a core crystallographic operation. Two sets of Cartesian coordinates of each point of a rotated object, those before and after rotation, are linearly related, and the coefficients of these linear combinations can be represented in matrix form. This 3 3...")
• 06:45, 1 August 2024 WikiSysop talk contribs created page 2024Gonzalez Dashboard (Created page with "== Citation == González-Rodriguez, Nayim / Areán-Ulloa, Emma / Fernández-Leiro, Rafael. A web-based dashboard for RELION metadata visualization. 2024. Acta Crystallographica Section D: Structural Biology, Vol. 80, No. 2 == Abstract == Cryo-electron microscopy (cryo-EM) has witnessed radical progress in the past decade, driven by developments in hardware and software. While current software packages include processing pipelines that simplify the imageprocessing work...")
• 06:19, 1 August 2024 WikiSysop talk contribs created page 2024Huang CryoNefen (Created page with "== Citation == Huang, Yue / Zhu, Chengguang / Yang, Xiaokang / Liu, Manhua. High-resolution real-space reconstruction of cryo-EM structures using a neural field network. 2024. Nature Machine Intelligence, p. 1-12 == Abstract == The elucidation of three-dimensional (3D) structures is crucial for unravelling the protein function and illuminating mechanisms in structural biology. Cryogenic electron microscopy (cryo-EM) single-particle analysis provides direct measurement...")
• 06:09, 1 August 2024 WikiSysop talk contribs created page 2024Beton Ensemble (Created page with "== Citation == Beton, Joseph G. / Mulvaney, Thomas / Cragnolini, Tristan / Topf, Maya. Cryo-EM structure and B-factor refinement with ensemble representation. 2024. Nature Communications, Vol. 15, No. 1, p. 444 == Abstract == Cryo-EM experiments produce images of macromolecular assemblies that are combined to produce three-dimensional density maps. Typically, atomic models of the constituent molecules are fitted into these maps, followed by a density-guided refinement...")
• 06:29, 31 July 2024 WikiSysop talk contribs created page 2024Mastronarded CTFPlotter (Created page with "== Citation == Mastronarde, David N. Accurate, automatic determination of astigmatism and phase with Ctfplotter in IMOD. 2024. J. Structural Biology, Vol. 216, No. 1, p. 108057 == Abstract == Ctfplotter in the IMOD software package is a flexible program for determination of CTF parameters in tilt series images. It uses a novel approach to find astigmatism by measuring defocus in one-dimensional power spectra rotationally averaged over a series of restricted angular ra...")