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Cryoelectron Microscopy

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CryoRes: Local Resolution Estimation of Cryo-EM Density Maps by Deep Learning.

Journal of molecular biology
Recent progress in cryo-EM research has ignited a revolution in biological macromolecule structure determination. Resolution is an essential parameter for quality assessment of a cryo-EM density map, and it is known that resolution varies in differen...

Cryo-electron Microscopy Reveals the Structure of the Nuclear Pore Complex.

Journal of molecular biology
The nuclear pore complex (NPC) is a giant protein assembly that penetrates the double layers of the nuclear membrane. The overall structure of the NPC has approximately eightfold symmetry and is formed by approximately 30 nucleoporins. The great size...

Applications and prospects of cryo-EM in drug discovery.

Military Medical Research
Drug discovery is a crucial part of human healthcare and has dramatically benefited human lifespan and life quality in recent centuries, however, it is usually time- and effort-consuming. Structural biology has been demonstrated as a powerful tool to...

Integrating Molecular Models Into CryoEM Heterogeneity Analysis Using Scalable High-resolution Deep Gaussian Mixture Models.

Journal of molecular biology
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with machine learning...

Deep learning for reconstructing protein structures from cryo-EM density maps: Recent advances and future directions.

Current opinion in structural biology
Cryo-Electron Microscopy (cryo-EM) has emerged as a key technology to determine the structure of proteins, particularly large protein complexes and assemblies in recent years. A key challenge in cryo-EM data analysis is to automatically reconstruct a...

Smart de novo Macromolecular Structure Modeling from Cryo-EM Maps.

Journal of molecular biology
The study of macromolecular structures has expanded our understanding of the amazing cell machinery and such knowledge has changed how the pharmaceutical industry develops new vaccines in recent years. Traditionally, X-ray crystallography has been th...

Improving Protein-Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge.

Biomolecules
Elucidating protein-ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein-ligand interaction is traditionally tackled by molecular docking a...

Mass-Spec, Cryo-EM and AI join forces for a close look at the transporter complex in cilia.

The EMBO journal
The intraflagellar transport (IFT) complex transports components between the cytoplasm and the ciliary tip. Two studies now report on the atomic structure of IFT-B, the core of IFT, using cutting-edge technology, such as cross-linking mass spectromet...

Multi-state modeling of antibody-antigen complexes with SAXS profiles and deep-learning models.

Methods in enzymology
Antibodies are an established class of human therapeutics. Epitope characterization is an important part of therapeutic antibody discovery. However, structural characterization of antibody-antigen complexes remains challenging. On the one hand, X-ray...

Deep Learning-Based Segmentation of Cryo-Electron Tomograms.

Journal of visualized experiments : JoVE
Cryo-electron tomography (cryo-ET) allows researchers to image cells in their native, hydrated state at the highest resolution currently possible. The technique has several limitations, however, that make analyzing the data it generates time-intensiv...