Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy
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 …
images of biomolecules frozen at cryogenic temperatures. A major advantage of this …
The ugly, bad, and good stories of large-scale biomolecular simulations
Molecular modeling of large biomolecular assemblies exemplifies a disruptive area holding
both promises and contentions. Propelled by peta and exascale computing, several …
both promises and contentions. Propelled by peta and exascale computing, several …
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction
Three-dimensional structure modeling from maps is an indispensable step for studying
proteins and their complexes with cryogenic electron microscopy. Although the resolution of …
proteins and their complexes with cryogenic electron microscopy. Although the resolution of …
Structural insights into the modulation of coronavirus spike tilting and infectivity by hinge glycans
Coronavirus spike glycoproteins presented on the virion surface mediate receptor binding,
and membrane fusion during virus entry and constitute the primary target for vaccine and …
and membrane fusion during virus entry and constitute the primary target for vaccine and …
CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2
B Shor, D Schneidman-Duhovny - Nature methods, 2024 - nature.com
Deep learning models, such as AlphaFold2 and RosettaFold, enable high-accuracy protein
structure prediction. However, large protein complexes are still challenging to predict due to …
structure prediction. However, large protein complexes are still challenging to predict due to …
Progressive assembly of multi-domain protein structures from cryo-EM density maps
Progress in cryo-electron microscopy has provided the potential for large-size protein
structure determination. However, the success rate for solving multi-domain proteins …
structure determination. However, the success rate for solving multi-domain proteins …
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 …
from cryo-EM data. It has been utilized for nearly two decades, and while cryo-EM resolution …
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 …
for near-atomic structure determination, shedding light on the important molecular …
Exploring cryo-electron microscopy with molecular dynamics
Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have
been complimentary methods since cryo-EM was first applied to the field of structural …
been complimentary methods since cryo-EM was first applied to the field of structural …
Computational biophysics meets cryo‐EM revolution in the search for the functional dynamics of biomolecular systems
There is a variety of experimental and computational techniques available to explore protein
dynamics, each presenting advantages and limitations. One promising experimental …
dynamics, each presenting advantages and limitations. One promising experimental …