Related papers: Computational Methods for Single-Particle Cryo-EM
Many imaging modalities involve reconstruction of unknown objects from collections of noisy projections related by random rotations. In one of these modalities, cryogenic electron microscopy (cryo-EM), the extremely low signal-to-noise…
Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here, we developed a refinement protocol based on Gaussian mixture models that integrates particle…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
In this paper, we provide assembly instructions for an easy to build experimental setup in order to gain practical experience with tomography. In view of this, this paper can be seen as a complementary work to excellent mathematical…
Cryo-electron tomography (cryo-ET) is an emerging technology for the 3D visualization of structural organizations and interactions of subcellular components at near-native state and sub-molecular resolution. Tomograms captured by cryo-ET…
Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. CryoEM provides direct visualization of individual macromolecules sampling different conformational and compositional states.…
A major challenge in single particle reconstruction from cryo-electron microscopy is to establish a reliable ab-initio three-dimensional model using two-dimensional projection images with unknown orientations. Common-lines based methods…
Cryo-electron tomography (cryo-ET) provides a unique window into molecular organization in cellular environments (in situ). However, the interpretation of molecular structural information is complicated by several intrinsic properties of…
Motivation: Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and…
Cryo-EM is a vital technique for determining 3D structure of biological molecules such as proteins and viruses. The cryo-EM reconstruction problem is challenging due to the high noise levels, the missing poses of particles, and the…
A crucial step in single particle analysis (SPA) of cryogenic electron microscopy (Cryo-EM), 2D classification and alignment takes a collection of noisy particle images to infer orientations and group similar images together. Averaging…
There is a clear need for developments in characterisation techniques that provide detailed information about structure-function relationships in biology. Using electron microscopy to achieve high resolution while maintaining a broad field…
We propose a framework to jointly determine the deformation parameters and reconstruct the unknown volume in electron cryotomography (CryoET). CryoET aims to reconstruct three-dimensional biological samples from two-dimensional projections.…
Cryogenic electron microscopy (cryo-EM) has become an enabling technology in drug discovery and in understanding molecular bases of disease by producing near-atomic resolution (less than 0.4 nm) 3D reconstructions of biological…
Electron cryo-microscopy (cryo-EM) produces three-dimensional (3D) maps of the electrostatic potential of biological macromolecules, including proteins. Along with knowledge about the imaged molecules, cryo-EM maps allow de novo atomic…
The cryo-electron microscope (cryo-EM) is increasingly popular these years. It helps to uncover the biological structures and functions of macromolecules. In this paper, we address image denoising problem in cryo-EM. Denoising the cryo-EM…
We show that de-focused single particle images recorded using a cryo-electron microscope (cryoEM) system may be processed like a Fresnel zone in-line hologram to obtain physically meaningful quantitative phase maps associated with…
In this report we study the problem of determining three-dimensional orientations for noisy projections of randomly oriented identical particles. The problem is of central importance in the tomographic reconstruction of the density map of…
Cryo-EM is a powerful tool for understanding macromolecular structures, yet current methods for structure reconstruction are slow and computationally demanding. To accelerate research on pose estimation, we present CESPED, a new dataset…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…