Present and emerging methodologies in cryo-EM single-particle analysis

M Wu, GC Lander - Biophysical journal, 2020 - cell.com
Over the past decade, technical and methodological improvements in cryogenic electron
microscopy (cryo-EM) single-particle analysis have enabled routine high-resolution …

Integrating model simulation tools and cryo‐electron microscopy

JG Beton, T Cragnolini, M Kaleel… - Wiley …, 2023 - Wiley Online Library
The power of computer simulations, including machine‐learning, has become an
inseparable part of scientific analysis of biological data. This has significantly impacted the …

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation

T Ginex, C Marco-Marín, M Wieczór, CP Mata… - PLoS …, 2022 - journals.plos.org
The S: A222V point mutation, within the G clade, was characteristic of the 20E (EU1) SARS-
CoV-2 variant identified in Spain in early summer 2020. This mutation has since reappeared …

Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome

K Kawakami, T Hamaguchi, Y Hirose, D Kosumi… - Nature …, 2022 - nature.com
Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes
(PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs …

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures

R Melero, COS Sorzano, B Foster, JL Vilas, M Martínez… - IUCrJ, 2020 - journals.iucr.org
Using a new consensus-based image-processing approach together with principal
component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in …

Juxtaposition of Bub1 and Cdc20 on phosphorylated Mad1 during catalytic mitotic checkpoint complex assembly

ES Fischer, CWH Yu, JF Hevler, SH McLaughlin… - Nature …, 2022 - nature.com
In response to improper kinetochore-microtubule attachments in mitosis, the spindle
assembly checkpoint (SAC) assembles the mitotic checkpoint complex (MCC) to inhibit the …

[HTML][HTML] EMDA: a python package for electron microscopy data analysis

R Warshamanage, K Yamashita… - Journal of Structural …, 2022 - Elsevier
An open-source Python library EMDA for cryo-EM map and model manipulation is presented
with a specific focus on validation. The use of several functionalities in the library is …

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 …

Simulation and machine learning methods for ion-channel structure determination, mechanistic studies and drug design

Z Zhu, Z Deng, Q Wang, Y Wang, D Zhang… - Frontiers in …, 2022 - frontiersin.org
Ion channels are expressed in almost all living cells, controlling the in-and-out
communications, making them ideal drug targets, especially for central nervous system …

Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches

O Miyashita, F Tama - Current Opinion in Structural Biology, 2023 - Elsevier
Flexible fitting based on molecular dynamics simulation is a technique for structure modeling
from cryo-EM data. It has been utilized for nearly two decades, and while cryo-EM resolution …