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A user with 2,423 edits. Account created on 30 March 2009.
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6 August 2024

5 August 2024

  • 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

2 August 2024

  • 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

1 August 2024

  • 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

31 July 2024

  • 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
  • 06:2806:28, 31 July 2024 diff hist +80 Main Page →CTF estimation and restoration
  • 06:2306:23, 31 July 2024 diff hist +928 N 2024Riggi Animation Created page with "== Citation == Riggi, Margot / Torrez, Rachel M. / Iwasa, Janet H. 3D animation as a tool for integrative modeling of dynamic molecular mechanisms. 2024. Structure, Vol. 32, No. 2, p. 122-130 == Abstract == As the scientific community accumulates diverse data describing how molecular mechanisms occur, creating and sharing visual models that integrate the richness of this information has become increasingly important to help us explore, refine, and communicate our hypo..." current
  • 06:2306:23, 31 July 2024 diff hist +98 Main Page →Books and reviews
  • 06:1106:11, 31 July 2024 diff hist +1,648 N 2024Feng DeepQs Created page with "== Citation == Feng, Ming-Feng / Chen, Yu-Xuan / Shen, Hong-Bin. DeepQs: Local quality assessment of cryo-EM density map by deep learning map-model fit score. 2024. J. Structural Biology, Vol. 216, No. 1, p. 108059 == Abstract == Cryogenic electron microscopy maps are valuable for determining macromolecule structures. A proper quality assessment method is essential for cryo-EM map selection or revision. This article presents DeepQs, a novel approach to estimate local..." current
  • 06:1006:10, 31 July 2024 diff hist +69 Main Page →Validation
  • 06:0106:01, 31 July 2024 diff hist +1,453 N 2023Sweeney ChemEM Created page with "== Citation == Sweeney, Aaron / Mulvaney, Thomas / Maiorca, Mauro / Topf, Maya. ChemEM: Flexible Docking of Small Molecules in Cryo-EM Structures. 2023. J. Medicinal Chemistry, Vol. 67, No. 1, p. 199-212 == Abstract == Cryo-electron microscopy (cryo-EM), through resolution advancements, has become pivotal in structure-based drug discovery. However, most cryo-EM structures are solved at 3−4 Å resolution, posing challenges for small-molecule docking and structure-bas..." current
  • 06:0006:00, 31 July 2024 diff hist +107 Main Page →Fitting and docking
  • 05:5405:54, 31 July 2024 diff hist +1,597 N 2024Yoshidome 4D Created page with "== Citation == Yoshidome, Takashi. Four-dimensional imaging for cryo-electron microscopy experiments using molecular simulations and manifold learning. 2024. J. Computational Chemistry, Vol. 45, No. 11, p. 738-751 == Abstract == Elucidating protein conformational changes is essential because conformational changes are closely related to the functions of proteins. Cryo-electron microscopy (cryo-EM) experiment can be used to reconstruct protein conformational changes vi..." current
  • 05:5305:53, 31 July 2024 diff hist +86 Main Page →3D Heterogeneity
  • 05:4405:44, 31 July 2024 diff hist +1,524 N 2023Fernandez Local Created page with "== Citation == Fernandez-Gimenez, Estrella / Carazo, J. M. / Sorzano, C. O. S. Local defocus estimation in single particle analysis in cryo-electron microscopy. 2023. J. Structural Biology, Vol. 215, No. 4, p. 108030 == Abstract == Single Particle analysis (SPA) aims to determine the three-dimensional structure of proteins and macromolecular complexes. The current state of the art has allowed us to achieve near-atomic and even atomic resolutions. To obtain high-resolu..." current
  • 05:4305:43, 31 July 2024 diff hist +66 Main Page →CTF estimation and restoration

30 July 2024

  • 06:1506:15, 30 July 2024 diff hist +1,751 N 2024deIsidro deep Created page with "== Citation == de Isidro-Gómez, Federico P. / Vilas, J. L. / Losana, P. / Carazo, J. M. / Sorzano, Carlos Oscar Sanchez. A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions. 2024. J. Structural Biology, Vol. 216, No. 1, p. 108056 == Abstract == Electron tomography is an imaging technique that allows for the elucidation of three-dimensional structural information of biological specimens in a very general..." current
  • 06:1506:15, 30 July 2024 diff hist +130 Main Page →Image alignment
  • 06:0106:01, 30 July 2024 diff hist +1,415 N 2023Zhu CryoSieve Created page with "== Citation == Zhu, Jianying / Zhang, Qi / Zhang, Hui / Shi, Zuoqiang / Hu, Mingxu / Bao, Chenglong. A minority of final stacks yields superior amplitude in single-particle cryo-EM. 2023. Nature Communications, Vol. 14, No. 1, p. 7822 == Abstract == Cryogenic electron microscopy (cryo-EM) is widely used to determine nearatomic resolution structures of biological macromolecules. Due to the low signal-to-noise ratio, cryo-EM relies on averaging many images. However, a c..." current
  • 06:0006:00, 30 July 2024 diff hist +97 Main Page →3D Reconstruction
  • 05:4805:48, 30 July 2024 diff hist +2,091 N 2022Kimanius Sparse Created page with "== Citation == Kimanius, Dari / Jamali, Kiarash / Scheres, Sjors. Sparse Fourier backpropagation in cryo-EM reconstruction. 2022. Advances in Neural Information Processing Systems, Vol. 35 p. 12395-12408 == Abstract == Electron cryo-microscopy (cryo-EM) is a powerful method for investigating the structures of protein molecules, with important implications for understanding the molecular processes of life and drug development. In this technique, many noisy, two-dimensi..." current
  • 05:4705:47, 30 July 2024 diff hist +77 Main Page →3D Reconstruction

29 July 2024

  • 05:4005:40, 29 July 2024 diff hist +1,527 N 2023Mendez Pipelines Created page with "== Citation == Mendez, Joshua H. / Chua, Eugene Y. D. / Paraan, Mohammadreza / Potter, Clinton S. / Carragher, Bridget. Automated pipelines for rapid evaluation during cryoEM data acquisition 2023. Current Opinion in Structural Biology, Vol. 83, p. 102729 == Abstract == Cryo-electron microscopy (cryoEM) has become a popular method for determining high-resolution structures of biomolecules. However, data processing can be time-consuming, particularly for new researcher..." current
  • 05:3905:39, 29 July 2024 diff hist +88 Main Page →Automated data collection

16 July 2024

  • 07:3007:30, 16 July 2024 diff hist +1,718 N 2024Parkhurst IceSimulation Created page with "== Citation == Parkhurst, James M. / Cavalleri, Anna / Dumoux, Maud / Basham, Mark / Clare, Daniel / Siebert, C. Alistair / Evans, Gwyndaf / Naismith, James H. / Kirkland, Angus / Essex, Jonathan W. Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples. 2024. Ultramicroscopy, Vol. 256, p. 113882 == Abstract == Simulations of cryo-electron microscopy (cryo-EM) images of biological samples can be used to produce test datas..." current
  • 07:2907:29, 16 July 2024 diff hist +127 Main Page →Image formation
  • 06:5306:53, 16 July 2024 diff hist +1,879 N 2021Himes Simulation Created page with "== Citation == Himes, Benjamin / Grigorieff, Nikolaus. Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation. 2021. IUCrJ, Vol. 8, No. 6, p. 943-953 == Abstract == Image simulation plays a central role in the development and practice of highresolution electron microscopy, including transmission electron microscopy of frozen-hydrated specimens (cryo-EM). Simulating images with contrast that matches the contrast observed in expe..." current
  • 06:5206:52, 16 July 2024 diff hist +114 Main Page →Image formation
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