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Cryo-EM reconstruction algorithms seek to determine a molecule's 3D density map from a series of noisy, unlabeled 2D projection images captured with an electron microscope.
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Maximum-likelihood multi-reference refinement for electron microscopy images
Sjors HW Scheres, Mikel Valle, Rafael Nuñez, Carlos OS Sorzano, Roberto Marabini, Gabor T Herman, and Jose-Maria Carazo · 2005
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Coarse-grained normal mode analysis in structural biology
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A Bayesian view on cryo-EM structure determination
Sjors H W Scheres · 2012
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Likelihood-based classification of cryo-EM images using FREALIGN
Lyumkis, Dmitry, Brilot, Axel F, Theobald, Douglas L, and Grigorieff, Nikolaus · 2013
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Bayesian analysis of individual electron microscopy images: Towards structures of dynamic and heterogeneous biomolecular assemblies
Pilar Cossio and Gerhard Hummer · 2013
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Iterative elastic 3d-to-2d alignment method using normal modes for studying structural dynamics of large macromolecular complexes
Qiyu Jin, Carlos Oscar S Sorzano, José Miguel De La Rosa-Trevín, José Román Bilbao-Castro, Rafael Núñez-Ramírez, Oscar Llorca, Florence Tama, and Slavica Jonić · 2014
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Thermodynamics of Coupled Protein Adsorption and Stability Using Hybrid Monte Carlo Simulations
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Anna Choromanska, Mikael Henaff, Michael Mathieu, Gérard Ben Arous, and Yann LeCun · 2015
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Enhanced sampling techniques in molecular dynamics simulations of biological systems
Rafael C Bernardi, Marcelo CR Melo, and Klaus Schulten · 2015
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The development of cryo-EM into a mainstream structural biology technique
Eva Nogales · 2016
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Continuous changes in structure mapped by manifold embedding of single-particle data in cryo-EM
Joachim Frank and Abbas Ourmazd · 2016
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cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
Ali Punjani, John L Rubinstein, David J Fleet, and Marcus A Brubaker · 2017
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Adam Paszke, Sam Gross, Francisco Massa, Adam Lerer, James Bradbury, Gregory Chanan, Trevor Killeen, Zeming Lin, Natalia Gimelshein, Luca Antiga, Alban Desmaison, Andreas Köpf, Edward Yang, Zach DeVito, Martin Raison, Alykhan Tejani, Sasank Chilamkurthy, Benoit Steiner, Lu Fang, Junjie Bai, and Soumith Chintala · 2019
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Enhanced sampling in molecular dynamics
Yi Isaac Yang, Qiang Shao, Jun Zhang, Lijiang Yang, and Yi Qin Gao · 2019
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De Novo Computational Protein Tertiary Structure Modeling Pipeline for Cryo-EM Maps of Intermediate Resolution
Daisuke Kihara, Genki Terashi, and Sai Raghavendra Maddhuri Venkata Subramaniya · 2020
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Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps
Dong Si, Spencer A Moritz, Jonas Pfab, Jie Hou, Renzhi Cao, Liguo Wang, Tianqi Wu, and Jianlin Cheng · 2020
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Computational Methods for Single-Particle Electron Cryomicroscopy
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Takanori Nakane, Dari Kimanius, Erik Lindahl, and Sjors Hw Scheres · 2018
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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, and Sjors H.W. Scheres · 2018
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cisTEM, user-friendly software for single-particle image processing
Timothy Grant, Alexis Rohou, and Nikolaus Grigorieff · 2018
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ISOLDE: A physically realistic environment for model building into low-resolution electron-density maps
Tristan Ian Croll · 2018
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Simultaneous determination of protein structure and dynamics using cryo-electron microscopy
Massimiliano Bonomi, Riccardo Pellarin, and Michele Vendruscolo · 2018
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Likelihood-based structural analysis of electron microscopy images
Pilar Cossio and Gerhard Hummer · 2018
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Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs
T Bepler, A Morin, M Rapp, J Brasch, and L Shapiro · 2019
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Structure, function, and antigenicity of the sars-cov-2 spike glycoprotein
Alexandra C Walls, Young-Jun Park, M Alejandra Tortorici, Abigail Wall, Andrew T McGuire, and David Veesler · 2020
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Reconstructing continuous distributions of 3D protein structure from cryo-EM images
Ellen D Zhong, Tristan Bepler, Joseph H Davis, and Bonnie Berger · 2020
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Hybrid electron microscopy normal mode analysis with scipion
Mohamad Harastani, Carlos Oscar S Sorzano, and Slavica Jonić · 2020
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DeepEMhancer: a deep learning solution for cryo-EM volume post-processing
R Sánchez-García, J Gomez-Blanco, A Cuervo, J M Carazo, COS Sorzano, and J Vargas · 2020
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CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks
Ellen D Zhong, Tristan Bepler, Bonnie Berger, and Joseph H Davis · 2021
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3d variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-em
Ali Punjani and David J Fleet · 2021
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Exploiting prior knowledge about biological macromolecules in cryo-em structure determination
Dari Kimanius, Gustav Zickert, Takanori Nakane, Jonas Adler, Sebastian Lunz, C-B Schönlieb, Ozan Öktem, and Sjors HW Scheres · 2021
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Inferring a continuous distribution of atom coordinates from cryo-em images using vaes, 2021
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