Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy

WS Tang, ED Zhong, SM Hanson, EH Thiede… - Current Opinion in …, 2023 - Elsevier
Single-particle cryo-electron microscopy (cryo-EM) is a technique that takes projection
images of biomolecules frozen at cryogenic temperatures. A major advantage of this …

Methods for cryo-EM single particle reconstruction of macromolecules having continuous heterogeneity

B Toader, FJ Sigworth, RR Lederman - Journal of molecular biology, 2023 - Elsevier
Macromolecules change their shape (conformation) in the process of carrying out their
functions. The imaging by cryo-electron microscopy of rapidly-frozen, individual copies of …

Integrating molecular models into CryoEM heterogeneity analysis using scalable high-resolution deep Gaussian mixture models

M Chen, B Toader, R Lederman - Journal of molecular biology, 2023 - Elsevier
Resolving the structural variability of proteins is often key to understanding the structure–
function relationship of those macromolecular machines. Single particle analysis using …

Exploring the structural variability of dynamic biological complexes by single-particle cryo-electron microscopy

MC DiIorio, AW Kulczyk - Micromachines, 2022 - mdpi.com
Biological macromolecules and assemblies precisely rearrange their atomic 3D structures to
execute cellular functions. Understanding the mechanisms by which these molecular …

Novel artificial intelligence-based approaches for ab initio structure determination and atomic model building for cryo-electron microscopy

MC DiIorio, AW Kulczyk - Micromachines, 2023 - mdpi.com
Single particle cryo-electron microscopy (cryo-EM) has emerged as the prevailing method
for near-atomic structure determination, shedding light on the important molecular …

Computational biophysics meets cryo‐EM revolution in the search for the functional dynamics of biomolecular systems

MGS Costa, M Gur, JM Krieger… - Wiley Interdisciplinary …, 2024 - Wiley Online Library
There is a variety of experimental and computational techniques available to explore protein
dynamics, each presenting advantages and limitations. One promising experimental …

Scaling up cryo-EM for biology and chemistry: The journey from niche technology to mainstream method

MJ de la Cruz, ET Eng - Structure, 2023 - cell.com
Cryoelectron microscopy (cryo-EM) methods have made meaningful contributions in a wide
variety of scientific research fields. In structural biology, cryo-EM routinely elucidates …

Beyond ManifoldEM: geometric relationships between manifold embeddings of a continuum of 3D molecular structures and their 2D projections

E Seitz, J Frank, P Schwander - Digital Discovery, 2023 - pubs.rsc.org
ManifoldEM is an established method of geometric machine learning developed to extract
information on conformational motions of molecules from their projections obtained by …

Temporal label recovery from noisy dynamical data

Y Khoo, XT Tong, W Wang, Y Wang - arXiv preprint arXiv:2406.13635, 2024 - arxiv.org
Analyzing dynamical data often requires information of the temporal labels, but such
information is unavailable in many applications. Recovery of these temporal labels, closely …

Energy landscapes from cryo-EM snapshots: a benchmarking study

R Dsouza, G Mashayekhi, R Etemadpour… - Scientific reports, 2023 - nature.com
Biomolecules undergo continuous conformational motions, a subset of which are
functionally relevant. Understanding, and ultimately controlling biomolecular function are …