Gctf: Real-time CTF determination and correction
TLDR
The main target of Gctf is to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra of observed micrographs after background subtraction to improve CTF parameters of all particles for subsequent image processing.About:
This article is published in Journal of Structural Biology.The article was published on 2016-01-01 and is currently open access. It has received 2919 citations till now. The article focuses on the topics: Background subtraction.read more
Citations
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cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
TL;DR: It is shown that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer.
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Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.
TL;DR: Cryo–electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter B0AT1 with or without the receptor binding domain (RBD) of the surface spike glycoprotein of SARS-CoV-2 are presented, providing important insights into the molecular basis for coronavirus recognition and infection.
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New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Jasenko Zivanov,Takanori Nakane,Björn O. Forsberg,Dari Kimanius,Wim J. H. Hagen,Erik Lindahl,Erik Lindahl,Sjors H.W. Scheres +7 more
TL;DR: CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations in the third major release of RELION.
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Cryo-EM structures of tau filaments from Alzheimer’s disease
Anthony W. P. Fitzpatrick,Benjamin Falcon,Shaoda He,Alexey G. Murzin,Garib N. Murshudov,Holly J. Garringer,R. Anthony Crowther,Bernardino Ghetti,Michel Goedert,Sjors H.W. Scheres +9 more
TL;DR: Scheres et al. as mentioned in this paper presented a 3.4-3.5-resolution image of the brain of an individual with Alzheimer's disease and showed that the protein cores are made of two identical protofilaments comprising residues 306-378 of tau protein.
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A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2.
Chi Xiangyang,Renhong Yan,Jun Zhang,Zhang Guanying,Yuanyuan Zhang,Hao Meng,Zhe Zhang,Pengfei Fan,Dong Yunzhu,Yilong Yang,Chen Zhengshan,Yingying Guo,Jinlong Zhang,Yaning Li,Xiaohong Song,Chen Yi,Lu Xia,Ling Fu,Lihua Hou,Junjie Xu,Changming Yu,Jianmin Li,Qiang Zhou,Wei Chen +23 more
TL;DR: The epitope of 4A8 is defined as the N-terminal domain (NTD) of the S protein by determining with cryo–eletron microscopy its structure in complex with the Sprotein, which points to the NTD as a promising target for therapeutic mAbs against COVID-19.
References
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RELION: implementation of a Bayesian approach to cryo-EM structure determination.
TL;DR: Developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined are described.
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CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou,Nikolaus Grigorieff +1 more
TL;DR: Modifications to the CTFFIND algorithm are described which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates.
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EMAN2: an extensible image processing suite for electron microscopy.
Guang Tang,Liwei Peng,Philip R. Baldwin,Deepinder S. Mann,Wen Jiang,I. Rees,Steven J. Ludtke +6 more
TL;DR: EMAN2 has been under development for the last two years, with a completely refactored image processing library, and a wide range of features to make it much more flexible and extensible than EMAN1.
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EMAN: semiautomated software for high-resolution single-particle reconstructions.
TL;DR: EMAN (Electron Micrograph ANalysis), a software package for performing semiautomated single-particle reconstructions from transmission electron micrographs, was written from scratch in C++ and is provided free of charge on the Web site.
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Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
Xueming Li,Paul Mooney,Shawn Q. Zheng,Shawn Q. Zheng,Christopher R. Booth,Michael B. Braunfeld,Michael B. Braunfeld,Sander Gubbens,David A. Agard,David A. Agard,Yifan Cheng +10 more
TL;DR: This approach determined a 3.3-Å-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density and greatly enhances image quality and data acquisition efficiency.