Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Video

Updated: Sep 23, 2025

Cryo-EM and Single-Particle Analysis with Scipion
09:06

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

4.0K

LPTD: a novel linear programming-based topology determination method for cryo-EM maps.

Bahareh Behkamal1, Mahmoud Naghibzadeh1, Andrea Pagnani2,3,4

  • 1Department of Computer Engineering, Faculty of Engineering, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran.

Bioinformatics (Oxford, England)
|May 13, 2022
PubMed
Summary

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 Novel Machine-Learning Based Method for Resolving Secondary Structure Topology in Medium-Resolution Cryo-EM Density Maps.

International journal of molecular sciences·2026
Same author

Determining acoustic impedance cube by inverting seismic data using feedforward and radial basis neural networks in an Iranian oilfield.

Scientific reports·2026
Same author

Investigating the source of acoustic anisotropy in the Asmari Formation, a fractured carbonate reservoir, using a well in the Southwest Iran.

Scientific reports·2025
Same author

A physics-informed deep learning approach for 3D acoustic impedance estimation from seismic data: application to an offshore field in the Southwest Iran.

Scientific reports·2025
Same author

A machine learning-based framework for predicting metabolic syndrome using serum liver function tests and high-sensitivity C-reactive protein.

Scientific reports·2025
Same author

RAS/RAF/MEK/MAPK signaling pathway as a therapeutic target in breast cancer: Emphasis on a novel carrier for tamoxifen and digestion behaviors.

Avicenna journal of phytomedicine·2025
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026
Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026
Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
See all related articles
This summary is machine-generated.

A new linear programming-based topology determination (LPTD) method accurately matches protein sequence elements to cryo-EM maps. This fast approach identifies native protein topology, even for complex structures with many secondary structure elements.

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Accurate protein structure determination from cryo-electron microscopy (cryo-EM) maps is crucial for understanding biological function.
  • Identifying the correct arrangement and orientation of secondary structure elements (SSEs) within a cryo-EM map, known as topology determination, is a critical and challenging step.
  • Existing methods struggle with the complexity and scale of modern protein structures.

Purpose of the Study:

  • To develop an automated and efficient method for accurate topology determination in medium-resolution cryo-EM data.
  • To address the challenge of matching secondary structure elements (SSEs) from a protein sequence to their corresponding locations and orientations in a 3D cryo-EM density map.
  • To provide a robust solution for complex protein structures with numerous SSEs.

More Related Videos

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

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

Published on: July 19, 2024

1.6K
Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition
08:16

Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition

Published on: March 19, 2021

4.6K

Related Experiment Videos

Last Updated: Sep 23, 2025

Cryo-EM and Single-Particle Analysis with Scipion
09:06

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

4.0K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

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

Published on: July 19, 2024

1.6K
Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition
08:16

Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition

Published on: March 19, 2021

4.6K

Main Methods:

  • Developed a linear programming-based topology determination (LPTD) method.
  • Modeled protein sequences and extracted reliable features.
  • Utilized a distance-based scoring function to transform the SSE matching problem into a weighted bipartite graph matching problem.
  • Employed a linear programming algorithm for decision-making to identify the native topology.

Main Results:

  • The LPTD method achieved high accuracy and speed in topology determination.
  • Native topology was identified as the top-ranked solution in 77% of test cases within 2 seconds.
  • Successfully handled complex proteins with up to 65 SSEs, surpassing the capabilities of current tools.
  • Validated on 12 experimental and 15 simulated alpha-beta proteins.

Conclusions:

  • LPTD offers a significant advancement in automated protein structure determination from cryo-EM data.
  • The method's efficiency and accuracy make it suitable for analyzing large and complex protein structures.
  • LPTD provides a reliable solution for the challenging problem of secondary structure topology determination.