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Related Experiment Video

Updated: Jan 8, 2026

Cryo-EM and Single-Particle Analysis with Scipion

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

Cryo-EM Analysis in CASP16.

Thomas Mulvaney^1,2, Andriy Kryshtafovych³, Maya Topf^1,2,4

¹Research Department of Integrative Virology, Leibniz Institute of Virology (LIV), Hamburg, Germany.

|December 11, 2025

Summary

This summary is machine-generated.

Cryo-electron microscopy (cryo-EM) data reveals local resolution correlates with protein flexibility in predictions. This finding aids in assessing atomic models and identifying discrepancies between predictions and experimental data.

Keywords:

CASP RNA structure cryo‐EM flexibility local resolution protein structure structure prediction

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Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

Experimentalists are encouraged to submit cryo-electron microscopy (cryo-EM) data and atomic models for assessment in CASP.
CASP16 saw 38 cryo-EM datasets submitted, representing most targets, often with a single atomic structure provided.

Purpose of the Study:

To investigate the relationship between local resolution in cryo-EM reconstructions and the flexibility of predicted protein structures.
To evaluate the accuracy of CASP predictions by comparing them with experimental cryo-EM data and local resolution information.

Main Methods:

Analysis of 38 cryo-EM datasets from CASP16.
Correlation analysis between local resolution in cryo-EM maps and root-mean-square fluctuations (RMSF) of residues in CASP predictions.
Assessment of sidechain details using a variant of SMOC with local fragment alignment.

Main Results:

Local resolution in cryo-EM reconstructions shows a good correlation with the root-mean-square fluctuations (RMSF) of residues in accurate CASP predictions.
The correlation between local resolution and pLDDT was less clear, particularly with mobile domains.
Assessment of sidechains revealed areas for improvement in high-quality predictions and identified modeling discrepancies in some targets.

Conclusions:

Local resolution in cryo-EM data serves as a valuable indicator of structural flexibility in predicted models.
Experimental cryo-EM data is crucial for model-free assessment, enabling unique analyses like comparison to local resolution.
Discrepancies between predictions and experimental density highlight areas where modeling needs refinement.