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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).
- 05:54, 31 July 2024 WikiSysop talk contribs created page 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...")
- 05:44, 31 July 2024 WikiSysop talk contribs created page 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...")
- 06:15, 30 July 2024 WikiSysop talk contribs created page 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...")
- 06:01, 30 July 2024 WikiSysop talk contribs created page 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...")
- 05:48, 30 July 2024 WikiSysop talk contribs created page 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...")
- 05:40, 29 July 2024 WikiSysop talk contribs created page 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...")
- 07:30, 16 July 2024 WikiSysop talk contribs created page 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...")
- 06:53, 16 July 2024 WikiSysop talk contribs created page 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...")
- 08:03, 15 July 2024 WikiSysop talk contribs created page 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...")
- 07:48, 15 July 2024 WikiSysop talk contribs created page 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...")
- 07:40, 15 July 2024 WikiSysop talk contribs created page 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...")
- 07:29, 15 July 2024 WikiSysop talk contribs created page 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...")
- 06:15, 12 July 2024 WikiSysop talk contribs created page 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...")
- 06:05, 12 July 2024 WikiSysop talk contribs created page 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...")
- 05:47, 12 July 2024 WikiSysop talk contribs created page 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...")
- 16:22, 11 July 2024 WikiSysop talk contribs created page 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...")
- 16:14, 11 July 2024 WikiSysop talk contribs created page 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...")
- 10:34, 5 April 2021 WikiSysop talk contribs moved page 2020Singer NonUniformKam to 2020Sharon NonUniformKam (The index is constructed using the first author)
- 19:21, 4 March 2021 WikiSysop talk contribs moved page 2019Ramirez LocalDeblur to 2020Ramirez LocalDeblur
- 20:28, 23 February 2021 WikiSysop talk contribs moved page 2020Matsumoto DEFmap to 2021Matsumoto DEFmap
- 18:49, 29 June 2020 User account Garygangren talk contribs was created by WikiSysop talk contribs and password was sent by email
- 06:26, 21 September 2019 User account Fsigworth talk contribs was created by WikiSysop talk contribs and password was sent by email
- 08:40, 27 May 2018 WikiSysop talk contribs moved page 2018Earl review to 2017Earl review
- 09:40, 10 May 2018 User account Javiervargas talk contribs was created by WikiSysop talk contribs and password was sent by email
- 07:24, 10 May 2018 User account Tmajtner talk contribs was created by WikiSysop talk contribs and password was sent by email
- 13:02, 19 April 2018 WikiSysop talk contribs moved page 2015Shan Multibody to 2016Shan Multibody
- 18:42, 7 October 2017 User account Coss talk contribs was created by WikiSysop talk contribs and password was sent by email
- 14:34, 7 September 2017 WikiSysop talk contribs deleted the user account "ArnauUser" (165)
- 14:34, 7 September 2017 WikiSysop talk contribs merged the user account "ArnauUser" (165) into Arnau (164)
- 14:18, 7 September 2017 WikiSysop talk contribs changed group membership for Arnau: granted bureaucrat; revoked administrator
- 14:12, 7 September 2017 User account Arnau talk contribs was created
- 14:09, 7 September 2017 WikiSysop talk contribs changed group membership for Arnau: granted administrator
- 14:05, 7 September 2017 User account Arnau talk contribs was created by WikiSysop talk contribs
- 11:38, 16 January 2017 User account Bzuber talk contribs was created by WikiSysop talk contribs
- 15:45, 24 October 2016 User account Matthewjessop talk contribs was created by WikiSysop talk contribs
- 15:45, 24 October 2016 User account Jvargas talk contribs was created by WikiSysop talk contribs
- 10:49, 18 October 2016 User account Danielcastano talk contribs was created by WikiSysop talk contribs
- 10:49, 18 October 2016 User account Lkova talk contribs was created by WikiSysop talk contribs
- 10:48, 18 October 2016 User account Rbehrouzi talk contribs was created by WikiSysop talk contribs
- 10:48, 18 October 2016 User account Dlyumkis talk contribs was created by WikiSysop talk contribs
- 10:47, 18 October 2016 User account Sjonic talk contribs was created by WikiSysop talk contribs
- 07:48, 5 October 2016 User account Mkikkawa talk contribs was created by WikiSysop talk contribs
- 15:10, 15 September 2016 User account CoSS2 talk contribs was created by WikiSysop talk contribs
- 15:08, 15 September 2016 User account Bionanopig talk contribs was created by WikiSysop talk contribs
- 15:08, 15 September 2016 User account Zaphod talk contribs was created by WikiSysop talk contribs
- 15:08, 15 September 2016 User account Gonenlab talk contribs was created by WikiSysop talk contribs
- 09:56, 22 April 2016 User account Tejal talk contribs was created by WikiSysop talk contribs
- 10:29, 28 December 2015 CoSS talk contribs moved page 2015Wu Review to 2016Wu Review