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 Concept Videos

Cryo-electron Microscopy01:28

Cryo-electron Microscopy

3.4K
Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
3.4K

You might also read

Related Articles

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

Sort by
Same author

Insights from aquaporin structures into drug-resistant sleeping sickness.

eLife·2026
Same author

Structure and organization of AMPA receptor-TARP complexes in the mammalian cerebellum.

Science (New York, N.Y.)·2025
Same author

The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge.

bioRxiv : the preprint server for biology·2025
Same author

Merging conformational landscapes in a single consensus space with FlexConsensus algorithm.

Nature methods·2025
Same author

ISG15 as a Potent Immune Adjuvant in MVA-Based Vaccines Against Zika Virus and SARS-CoV-2.

Vaccines·2025
Same author

Structural analysis of HER2-trastuzumab complex reveals receptor conformational adaptation.

Science advances·2025

Related Experiment Video

Updated: Jul 15, 2025

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

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

3.8K

Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling

James M Krieger1, Carlos Oscar S Sorzano1, Jose Maria Carazo1

  • 1Biocomputing Unit, National Centre for Biotechnology (CNB CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, Cantoblanco, 28049 Madrid, Spain.

International Journal of Molecular Sciences
|September 28, 2023
PubMed
Summary

This study integrates the ProDy Python API into the Scipion workflow engine, enhancing access to macromolecular dynamics analysis for a broader user base. The Scipion-EM-ProDy plugin offers advanced computational tools for studying protein dynamics.

Keywords:
cryo-electron microscopyelastic network modelsensemble analysisglobal protein dynamicshybrid simulationsnormal mode analysisprincipal component analysissoftware integration workflows

More Related Videos

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion
13:43

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

Published on: January 31, 2022

13.3K
High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE
13:28

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

Published on: May 16, 2017

50.4K

Related Experiment Videos

Last Updated: Jul 15, 2025

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

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

3.8K
A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion
13:43

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

Published on: January 31, 2022

13.3K
High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE
13:28

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

Published on: May 16, 2017

50.4K

Area of Science:

  • Computational structural biology
  • Biophysics
  • Bioinformatics

Background:

  • Macromolecular assemblies exhibit dynamic structural changes crucial for their biological functions.
  • Elastic Network Model (ENM) normal mode analysis and Principal Component Analysis (PCA) are key computational methods for studying these dynamics.
  • Current tools often require advanced programming skills, limiting accessibility.

Purpose of the Study:

  • To integrate the ProDy Python API into the Scipion workflow engine.
  • To provide a wider range of users with access to advanced macromolecular dynamics analysis tools.
  • To enable the creation of complex computational pipelines for studying protein dynamics.

Main Methods:

  • Integration of the ProDy Python application programming interface (API) into the Scipion workflow engine.
  • Development of new protocols and pipelines within the Scipion framework.
  • Leveraging existing functionalities of ProDy for conformational sampling and dynamics analysis.

Main Results:

  • The Scipion-EM-ProDy plugin provides enhanced functionality for macromolecular dynamics analysis.
  • Wider accessibility to advanced computational tools for researchers without extensive programming expertise.
  • Facilitation of integration with other software packages for cryo-electron microscopy and molecular simulations.

Conclusions:

  • The Scipion-EM-ProDy plugin democratizes access to sophisticated protein dynamics analysis.
  • This integration empowers a broader scientific community to explore complex macromolecular behaviors.
  • The developed plugin enhances the capabilities of the Scipion platform for structural biology research.