Cryogenic electron microscopy and single-particle analysis

D Elmlund, H Elmlund - Annual review of biochemistry, 2015‏ - annualreviews.org
About 20 years ago, the first three-dimensional (3D) reconstructions at subnanometer (< 10-
Å) resolution of an icosahedral virus assembly were obtained by cryogenic electron …

Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization

SHW Scheres, H Gao, M Valle, GT Herman… - Nature …, 2007‏ - nature.com
Although three-dimensional electron microscopy (3D-EM) permits structural characterization
of macromolecular assemblies in distinct functional states, the inability to classify projections …

An introduction to maximum-likelihood methods in cryo-EM

FJ Sigworth, PC Doerschuk, JM Carazo… - Methods in …, 2010‏ - Elsevier
The maximum-likelihood method provides a powerful approach to many problems in cryo-
electron microscopy (cryo-EM) image processing. This contribution aims to provide an …

Classification of structural heterogeneity by maximum-likelihood methods

SHW Scheres - Methods in enzymology, 2010‏ - Elsevier
With the advent of computationally feasible approaches to maximum-likelihood (ML) image
processing for cryo-electron microscopy, these methods have proven particularly useful in …

Modeling experimental image formation for likelihood-based classification of electron microscopy data

SHW Scheres, R Núñez-Ramírez, Y Gómez-Llorente… - Structure, 2007‏ - cell.com
The coexistence of multiple distinct structural states often obstructs the application of three-
dimensional cryo-electron microscopy to large macromolecular complexes. Maximum …

[HTML][HTML] In vivo assembly of an archaeal virus studied with whole-cell electron cryotomography

C Fu, K Wang, L Gan, J Lanman, R Khayat, MJ Young… - Structure, 2010‏ - cell.com
We applied whole-cell electron cryotomography to the archaeon Sulfolobus infected by
Sulfolobus turreted icosahedral virus (STIV), which belongs to the PRD1-Adeno lineage of …

Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps

Q Wang, T Matsui, T Domitrovic, Y Zheng… - Journal of structural …, 2013‏ - Elsevier
CryoEM data capture the dynamic character associated with biological macromolecular
assemblies by preserving the various conformations of the individual specimens at the …

Unified 3-D structure and projection orientation refinement using quasi-Newton algorithm

C Yang, EG Ng, PA Penczek - Journal of structural biology, 2005‏ - Elsevier
We describe an algorithm for simultaneous refinement of a three-dimensional (3-D) density
map and of the orientation parameters of two-dimensional (2-D) projections that are used to …

An adaptive expectation–maximization algorithm with GPU implementation for electron cryomicroscopy

HD Tagare, A Barthel, FJ Sigworth - Journal of structural biology, 2010‏ - Elsevier
Maximum-likelihood (ML) estimation has very desirable properties for reconstructing 3D
volumes from noisy cryo-EM images of single macromolecular particles. Current …

Maximum likelihood refinement of electron microscopy data with normalization errors

SHW Scheres, M Valle, P Grob, E Nogales… - Journal of structural …, 2009‏ - Elsevier
Commonly employed data models for maximum likelihood refinement of electron
microscopy images behave poorly in the presence of normalization errors. Small variations …