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A user with 2,486 edits. Account created on 30 March 2009.
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31 July 2024

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

15 July 2024

  • 08:0308:03, 15 July 2024 diff hist +1,915 N 2023Richardson Overfitting Created page with "== Citation == Richardson, Jane S. / Williams, Christopher J. / Chen, Vincent B. / Prisant, Michael G. / Richardson, David C. The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions. 2023. Acta Crystallographica Section D: Structural Biology, Vol. 79, No. 12 == Abstract == Model building and refinement, and the validation of their correctness, are very effective and..." current
  • 08:0208:02, 15 July 2024 diff hist +99 Main Page →Fitting and docking
  • 07:4807:48, 15 July 2024 diff hist +1,912 N 2024Yadav Orientation Created page with "== Citation == Yadav, Swati / Vinothkumar, Kutti R. Factors affecting macromolecule orientations in thin films formed in cryo-EM. 2024. Acta Crystallographica Section D: Structural Biology, Vol. 80, No. 7, p. 535-550 == Abstract == The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described near..." current
  • 07:4607:46, 15 July 2024 diff hist +98 Main Page →Sample preparation
  • 07:4007:40, 15 July 2024 diff hist +1,632 N 2024Hou Marker Created page with "== Citation == Hou, Gaoxin / Yang, Zhidong / Zang, Dawei / Fernández, Jose-Jesus / Zhang, Fa / Han, Renmin. MarkerDetector: A method for robust fiducial marker detection in electron micrographs using wavelet-based template. 2024. Journal of Structural Biology, Vol. 216, No. 1, p. 108044 == Abstract == Fiducial marker detection in electron micrographs becomes an important and challenging task with the development of large-field electron microscopy. The fiducial marker..." current
  • 07:3907:39, 15 July 2024 diff hist +68 Main Page →Image alignment
  • 07:2907:29, 15 July 2024 diff hist +1,502 N 2024Dickerson magnification Created page with "== Citation == Dickerson, Joshua L. / Leahy, Erin / Peet, Mathew J. / Naydenova, Katerina / Russo, Christopher J. Accurate magnification determination for cryoEM using gold. 2024. Ultramicroscopy , Vol. 256, p. 113883 == Abstract == Determining the correct magnified pixel size of single-particle cryoEM micrographs is necessary to maximize resolution and enable accurate model building. Here we describe a simple and rapid procedure for determining the absolute magnifica..." current
  • 07:2807:28, 15 July 2024 diff hist +100 Main Page →Image formation

12 July 2024

  • 06:1506:15, 12 July 2024 diff hist +1,547 N 2024Gao DomainFit Created page with "== Citation == Gao, Jerry / Tong, Maxwell / Lee, Chinkyu / Gaertig, Jacek / Legal, Thibault / Bui, Khanh Huy. DomainFit: Identification of protein domains in cryo-EM maps at intermediate resolution using AlphaFold2-predicted models. 2024. Structure, Vol. 32, p. 1-12 == Abstract == Cryoelectron microscopy (cryo-EM) has revolutionized the structural determination of macromolecular complexes. With the paradigm shift to structure determination of highly complex endogenous..." current
  • 06:1406:14, 12 July 2024 diff hist +127 Main Page →Segmentation
  • 06:0506:05, 12 July 2024 diff hist +1,556 N 2023Li Classification Created page with "== Citation == Li, Daoyi / Jiang, Wen. Classification of helical polymers with deep-learning language models. 2023. J. Structural Biology, Vol. 215, No. 4, p. 108041 == Abstract == Many macromolecules in biological systems exist in the form of helical polymers. However, the inherent polymorphism and heterogeneity of samples complicate the reconstruction of helical polymers from cryo-EM images. Currently, available 2D classification methods are effective at separating..." current
  • 06:0406:04, 12 July 2024 diff hist +101 Main Page →Filament picking
  • 05:4705:47, 12 July 2024 diff hist +1,671 N 2023Terwilliger AlphaFold Created page with "== Citation == Terwilliger, Thomas C. / Liebschner, Dorothee / Croll, Tristan I. / Williams, Christopher J. / McCoy, Airlie J. / Poon, Billy K. / Afonine, Pavel V. / Oeffner, Robert D. / Richardson, Jane S. / Read, Randy J. / others. AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination. 2024. Nature Methods, Vol. 21, No. 1, p. 110-116 == Abstract == Artificial intelligence-based protein structure predict..." current
  • 05:4305:43, 12 July 2024 diff hist +117 Main Page →Fitting and docking

11 July 2024

  • 16:2216:22, 11 July 2024 diff hist +1,424 N 2023McMullan 100kV Created page with "== Citation == McMullan, Greg / Naydenova, Katerina / Mihaylov, Daniel / Yamashita, Keitaro / Peet, Mathew J. / Wilson, Hugh / Dickerson, Joshua L. / Chen, Shaoxia / Cannone, Giuseppe / Lee, Yang / others. Structure determination by cryoEM at 100 keV. 2023. Proc. Natl. Acad. Sci. USA , Vol. 120, No. 49, p. e2312905120 == Abstract == Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, spec..." current
  • 16:2116:21, 11 July 2024 diff hist +56 Main Page →Image formation
  • 16:1416:14, 11 July 2024 diff hist +2,214 N 2024Herre Capsules Created page with "== Citation == Herre, Carol / Ho, Alex / Eisenbraun, Ben / Vincent, James / Nicholson, Thomas / Boutsioukis, Giorgos / Meyer, Peter A. / Ottaviano, Michelle / Krause, Kurt L. / Key, Jason / Sliz, Piotr. Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection. 2024-06. Acta crystallographica. Section D, Structural biology, Vol. 80, p. 439-450 == Abstract == The expansive scientific software ecosystem, char..." current
  • 16:1116:11, 11 July 2024 diff hist +103 Main Page →Software

20 June 2024

19 January 2024

17 January 2024

15 January 2024

12 January 2024

10 January 2024

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