User contributions for WikiSysop

Results for WikiSysop talk block log uploads logs
A user with 2,380 edits. Account created on 30 March 2009.
Jump to navigation Jump to search
Search for contributionsExpandCollapse
⧼contribs-top⧽
⧼contribs-date⧽
(newest | oldest) View ( | ) (20 | 50 | 100 | 250 | 500)

12 August 2024

9 August 2024

  • 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

8 August 2024

  • 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
  • 06:0206:02, 8 August 2024 diff hist +1,957 N 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..." current
  • 06:0106:01, 8 August 2024 diff hist +117 Main Page →3D Heterogeneity
  • 05:5405:54, 8 August 2024 diff hist +1,947 N 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..." current
  • 05:5205:52, 8 August 2024 diff hist +71 Main Page →3D Alignment
  • 05:4105:41, 8 August 2024 diff hist +1,171 N 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..." current
  • 05:4005:40, 8 August 2024 diff hist +106 Main Page →3D Alignment

7 August 2024

  • 08:1108:11, 7 August 2024 diff hist +1,959 N 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..." current
  • 08:1008:10, 7 August 2024 diff hist +73 Main Page →Sample preparation
  • 06:5206:52, 7 August 2024 diff hist +1,785 N 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..." current
  • 06:5106:51, 7 August 2024 diff hist +91 Main Page →Subtomogram analysis
  • 06:4206:42, 7 August 2024 diff hist +2,124 N 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..." current
  • 06:4106:41, 7 August 2024 diff hist +85 Main Page →3D Heterogeneity
  • 06:2406:24, 7 August 2024 diff hist +2,041 N 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..." current
  • 06:2306:23, 7 August 2024 diff hist +90 Main Page →2D Classification and clustering
  • 06:1806:18, 7 August 2024 diff hist +1,539 N 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..." current
  • 06:1706:17, 7 August 2024 diff hist +114 Main Page →3D Alignment
  • 06:1506:15, 7 August 2024 diff hist +1,872 N 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..." current
  • 06:0806:08, 7 August 2024 diff hist +97 Main Page →Software
(newest | oldest) View ( | ) (20 | 50 | 100 | 250 | 500)
Retrieved from "https://3demmethods.i2pc.es/index.php/Special:Contributions/WikiSysop"