Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: Mar 8, 2026

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps.

Dong Si¹, Jing He²

¹Division of Computing and Software Systems, University of Washington Bothell, Bothell, WA 98011, USA.

Biomed Research International

|February 7, 2017

Summary

This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

A Large-Scale Cryo-EM RNA Motif Dataset and Benchmark for Machine Learning-Based Structure Modeling.

bioRxiv : the preprint server for biology·2026

Same author

A Data Set of Paired Structural Segments Between Protein Data Bank and AlphaFold DB for Medium-Resolution Cryo-EM Density Maps: A Gap in Overall Structural Quality.

Bioinformatics research and applications : ... international symposium, ISBRA ... proceedings. ISBRA (Conference)·2026

Same author

Decoys Reveal Multiple Basins of Attraction for Cryo-Electron-Microscopy Flexible Fitting.

Computational structural bioinformatics : international workshop, CSBW 2024, Boston, MA, USA, November 16, 2024, proceeding. Computational Structural Bioinformatics Workshop (2024 : Boston, Mass.)·2025

Same author

Toward Modeling Protein Multimers by Combining AlphaFold 3 Predictions with Secondary Structures from Medium-Resolution Cryo-EM Maps.

Computational structural bioinformatics : international workshop, CSBW 2024, Boston, MA, USA, November 16, 2024, proceeding. Computational Structural Bioinformatics Workshop (2024 : Boston, Mass.)·2025

Same author

GOBoost: leveraging long-tail gene ontology terms for accurate protein function prediction.

Bioinformatics (Oxford, England)·2025

Same author

Beyond current boundaries: Integrating deep learning and AlphaFold for enhanced protein structure prediction from low-resolution cryo-EM maps.

Computational biology and chemistry·2025

Detecting beta-strands in cryo-electron microscopy (cryo-EM) density maps is challenging. A new method, StrandRoller, effectively models beta-strand traces in beta-barrels from cryo-EM data.

Area of Science:

Structural biology
Biophysics
Computational biology

Background:

Cryo-electron microscopy (cryo-EM) yields protein density maps at various resolutions.
Detecting alpha-helices is feasible at 5-8 Å resolution, but beta-strand detection remains difficult due to their close spacing and varied sheet shapes.

Purpose of the Study:

To develop and evaluate a novel computational approach for modeling beta-strand traces within beta-barrel structures from cryo-EM density maps.
To improve the accuracy and efficiency of secondary structure identification in low-to-medium resolution cryo-EM data.

Main Methods:

The study introduces StrandRoller, a new method designed to model beta-strand traces specifically for beta-barrel regions identified in cryo-EM density maps.
The method was tested on eight beta-barrel datasets derived from experimental cryo-EM maps with resolutions ranging from 5.5 Å to 8.25 Å.

More Related Videos

Author Spotlight: Optimizing Cryo-EM Analysis with CryoSieve for Enhanced Particle Selection Efficiency

Author Spotlight: Optimizing Cryo-EM Analysis with CryoSieve for Enhanced Particle Selection Efficiency

Published on: May 10, 2024

Cryo-EM and Single-Particle Analysis with Scipion

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

Related Experiment Videos

Last Updated: Mar 8, 2026

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Author Spotlight: Optimizing Cryo-EM Analysis with CryoSieve for Enhanced Particle Selection Efficiency

Author Spotlight: Optimizing Cryo-EM Analysis with CryoSieve for Enhanced Particle Selection Efficiency

Published on: May 10, 2024

Cryo-EM and Single-Particle Analysis with Scipion

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

Main Results:

StrandRoller successfully detected approximately 74.26% of amino acids belonging to beta-strands within the tested beta-barrel structures.
The method achieved an average 2-way distance of 2.05 Å between the modeled beta-strand traces and the actual observed traces, considering the best of fifteen detection scenarios.

Conclusions:

The proposed StrandRoller method demonstrates significant capability in accurately modeling beta-strand traces from cryo-EM density maps, particularly within beta-barrel regions.
This advancement addresses a key challenge in cryo-EM data analysis, facilitating more precise structural determination of proteins containing beta-sheet structures.