User contributions for WikiSysop

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

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
05:5005:50, 7 August 2024 diff hist +1,047 N 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..." current
05:4905:49, 7 August 2024 diff hist +67 Main Page →Noise reduction

07:0107:01, 6 August 2024 diff hist +2,078 N 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..." current
07:0007:00, 6 August 2024 diff hist +65 Main Page →Automatic particle picking
06:5406:54, 6 August 2024 diff hist +933 N 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..." current
06:5306:53, 6 August 2024 diff hist +51 Main Page →Databases
06:4306:43, 6 August 2024 diff hist +2,064 N 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..." current
06:4206:42, 6 August 2024 diff hist +121 Main Page →3D Alignment

06:2606:26, 5 August 2024 diff hist +1,505 N 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..." current
06:2606:26, 5 August 2024 diff hist +76 Main Page →Fitting and docking
06:0406:04, 5 August 2024 diff hist +1,783 N 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..." current
06:0306:03, 5 August 2024 diff hist +97 Main Page →Software
05:5605:56, 5 August 2024 diff hist +1,337 N 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..." current
05:5505:55, 5 August 2024 diff hist +136 Main Page →Fitting and docking
05:4405:44, 5 August 2024 diff hist +2,106 N 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..." current
05:4305:43, 5 August 2024 diff hist +112 Main Page →3D Reconstruction

06:1206:12, 2 August 2024 diff hist +2,100 N 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..." current
06:1106:11, 2 August 2024 diff hist +78 Main Page →Subtomogram analysis
06:0606:06, 2 August 2024 diff hist +1,866 N 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..." current
06:0406:04, 2 August 2024 diff hist 0 Main Page →Software
06:0306:03, 2 August 2024 diff hist +63 Main Page →Software
05:5905:59, 2 August 2024 diff hist +1,085 N 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,..." current
05:5505:55, 2 August 2024 diff hist +108 Main Page →Databases
05:4205:42, 2 August 2024 diff hist +1,998 N 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..." current
05:4105:41, 2 August 2024 diff hist +75 Main Page →Books and reviews

06:4506:45, 1 August 2024 diff hist +1,411 N 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..." current
06:4306:43, 1 August 2024 diff hist +77 Main Page →Software
06:1906:19, 1 August 2024 diff hist +1,665 N 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..." current
06:1606:16, 1 August 2024 diff hist +94 Main Page →3D Reconstruction
06:0906:09, 1 August 2024 diff hist +1,500 N 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..." current
06:0606:06, 1 August 2024 diff hist +57 Main Page →Fitting and docking

06:2906:29, 31 July 2024 diff hist +1,586 N 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..." current

User contributions for WikiSysop

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