Search Results - "Journal of structural biology"

3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM by Punjani, Ali, Fleet, David J.

“…[Display omitted] •Continuous structural heterogeneity of proteins is often functionally relevant.•Existing single particle cryo-EM reconstruction algorithms…”
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Gctf: Real-time CTF determination and correction by Zhang, Kai

“…Accurate estimation of the contrast transfer function (CTF) is critical for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction. Here, a…”
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CTFFIND4: Fast and accurate defocus estimation from electron micrographs by Rohou, Alexis, Grigorieff, Nikolaus

“…CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are…”
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Helical reconstruction in RELION by He, Shaoda, Scheres, Sjors H.W.

“…We describe a new implementation for the reconstruction of helical assemblies in the empirical Bayesian framework of RELION. Our approach calculates optimal…”
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Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging by Hagen, Wim J.H., Wan, William, Briggs, John A.G.

“…Cryo-electron tomography (cryoET) allows 3D structural information to be obtained from cells and other biological samples in their close-to-native state. In…”
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Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy by de la Rosa-Trevín, J.M., Quintana, A., del Cano, L., Zaldívar, A., Foche, I., Gutiérrez, J., Gómez-Blanco, J., Burguet-Castell, J., Cuenca-Alba, J., Abrishami, V., Vargas, J., Otón, J., Sharov, G., Vilas, J.L., Navas, J., Conesa, P., Kazemi, M., Marabini, R., Sorzano, C.O.S., Carazo, J.M.

“…In the past few years, 3D electron microscopy (3DEM) has undergone a revolution in instrumentation and methodology. One of the central players in this…”
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RELION: Implementation of a Bayesian approach to cryo-EM structure determination by Scheres, Sjors H.W.

“…RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis…”
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Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4 Å by Turoňová, Beata, Schur, Florian K.M., Wan, William, Briggs, John A.G.

“…Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular complexes to be imaged in three-dimensions in their native environments…”
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AIM2 inflammasome activation and regulation: A structural perspective by Wang, Bing, Yin, Qian

“…Absent in melanoma 2 (AIM2) inflammasome is a multi-protein platform that recognizes aberrant cytoplasmic dsDNA and induces cytokine maturation, release and…”
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Semi-automated selection of cryo-EM particles in RELION-1.3 by Scheres, Sjors H.W.

“…The selection of particles suitable for high-resolution cryo-EM structure determination from noisy micrographs may represent a tedious and time-consuming step…”
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Focus: The interface between data collection and data processing in cryo-EM by Biyani, Nikhil, Righetto, Ricardo D., McLeod, Robert, Caujolle-Bert, Daniel, Castano-Diez, Daniel, Goldie, Kenneth N., Stahlberg, Henning

“…We present a new software package called Focus that interfaces cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing…”
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Alignment of cryo-EM movies of individual particles by optimization of image translations by Rubinstein, John L., Brubaker, Marcus A.

“…Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum…”
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Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins by Schaffer, Miroslava, Mahamid, Julia, Engel, Benjamin D., Laugks, Tim, Baumeister, Wolfgang, Plitzko, Jürgen M.

“…While cryo-electron tomography (cryo-ET) can reveal biological structures in their native state within the cellular environment, it requires the production of…”
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UCSF Chimera, MODELLER, and IMP: An integrated modeling system by Yang, Zheng, Lasker, Keren, Schneidman-Duhovny, Dina, Webb, Ben, Huang, Conrad C., Pettersen, Eric F., Goddard, Thomas D., Meng, Elaine C., Sali, Andrej, Ferrin, Thomas E.

“…Structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. Here we present the integration of several…”
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Investigating interactions of the Bacillus subtilis spore coat proteins CotY and CotZ using single molecule force spectroscopy by Liu, Huiqing, Krajcikova, Daniela, Zhang, Zhe, Wang, Hongda, Barak, Imrich, Tang, Jilin

“…Spores formed by Bacillus subtilis are surrounded by a protective and multilayered shell, termed the coat, which grants the spores resistance to various…”
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DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM by Wang, Feng, Gong, Huichao, Liu, Gaochao, Li, Meijing, Yan, Chuangye, Xia, Tian, Li, Xueming, Zeng, Jianyang

“…Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck…”
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Spotiton: New features and applications by Dandey, Venkata P., Wei, Hui, Zhang, Zhening, Tan, Yong Zi, Acharya, Priyamvada, Eng, Edward T., Rice, William J., Kahn, Peter A., Potter, Clinton S., Carragher, Bridget

“…We present an update describing new features and applications of Spotiton, a novel instrument for vitrifying samples for cryoEM. We have used Spotiton to…”
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A structural analysis of M protein in coronavirus assembly and morphology by Neuman, Benjamin W., Kiss, Gabriella, Kunding, Andreas H., Bhella, David, Baksh, M. Fazil, Connelly, Stephen, Droese, Ben, Klaus, Joseph P., Makino, Shinji, Sawicki, Stanley G., Siddell, Stuart G., Stamou, Dimitrios G., Wilson, Ian A., Kuhn, Peter, Buchmeier, Michael J.

“…The M protein of coronavirus plays a central role in virus assembly, turning cellular membranes into workshops where virus and host factors come together to…”
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A streamlined workflow for automated cryo focused ion beam milling by Tacke, Sebastian, Erdmann, Philipp, Wang, Zhexin, Klumpe, Sven, Grange, Michael, Plitzko, Jürgen, Raunser, Stefan

“…[Display omitted] •Automated high-quality, high-throughput cryo-FIB milling.•Glove box and a cryo transfer system for optimal sample preparation and…”
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One number does not fit all: Mapping local variations in resolution in cryo-EM reconstructions by Cardone, Giovanni, Heymann, J. Bernard, Steven, Alasdair C.

“…The resolution of density maps from single particle analysis is usually measured in terms of the highest spatial frequency to which consistent information has…”
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