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Related Experiment Video

Updated: Sep 6, 2025

Cryo-EM and Single-Particle Analysis with Scipion

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

Sequence-assignment validation in cryo-EM models with checkMySequence.

Grzegorz Chojnowski¹

¹European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.

Acta Crystallographica. Section D, Structural Biology

|July 1, 2022

Summary

This summary is machine-generated.

A new automated tool, checkMySequence, detects errors in protein models built from cryo-electron microscopy (cryo-EM) maps. This method aids structural biologists by identifying sequence register shifts, improving model accuracy.

Keywords:

checkMySequence cryo-EM model validation register shifts sequence assignment

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A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

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Last Updated: Sep 6, 2025

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Structural biology
Computational biology
Biophysics

Background:

Artificial intelligence (AI) tools have advanced protein structure prediction and cryo-electron microscopy (cryo-EM) map interpretation.
Despite AI advancements, challenges remain in cryo-EM map interpretation, including identifying and correcting errors like sequence register shifts in protein models.
Manual refinement and visual inspection are still necessary but prone to occasional errors.

Purpose of the Study:

To introduce checkMySequence, a novel, automated, and parameter-free computational method for detecting sequence register shifts in protein models within cryo-EM maps.
To demonstrate the utility of checkMySequence in assisting with model building, particularly in low-resolution cryo-EM maps where visual interpretation is difficult.
To highlight how checkMySequence could have prevented a significant sequence-register error in a SARS-CoV-2 RNA-dependent RNA polymerase model.

Main Methods:

Development of checkMySequence, a fast and fully automated algorithm.
Parameter-free implementation, requiring no user-defined settings.
Application of checkMySequence to validate protein models built into cryo-EM density maps.

Main Results:

checkMySequence successfully detects sequence register shifts in protein models derived from cryo-EM data.
The method proves effective in aiding model building, especially when cryo-EM map resolution is suboptimal.
The tool could have identified a previously discovered, widely discussed sequence-register error in a SARS-CoV-2 RNA-dependent RNA polymerase model, preventing its propagation.

Conclusions:

checkMySequence offers a reliable and efficient solution for identifying sequence register shifts in cryo-EM-based protein models.
The software enhances the accuracy and integrity of structural models derived from cryo-EM data.
Automated error detection tools like checkMySequence are crucial for advancing structural biology and ensuring the reliability of published structural data.