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

RNA Structure01:23

RNA Structure

81.3K
Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
81.3K
Nucleic Acid Structure01:25

Nucleic Acid Structure

10.3K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
10.3K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

5.7K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
5.7K

You might also read

Related Articles

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

Sort by
Same author

PEP-EDIT: a web server for the 3D generation and interactive editing of complex peptides.

Nucleic acids research·2026
Same author

Statistical Molecular Interaction Fields: A Fast and Informative Tool for Characterizing RNA and Protein-Binding Pockets.

Journal of chemical theory and computation·2025
Same author

Author Correction: Identification of new ClpC1-NTD binders for Mycobacterium tuberculosis drug development.

Scientific reports·2025
Same author

Identification of new ClpC1-NTD binders for Mycobacterium tuberculosis drug development.

Scientific reports·2025
Same author

Molecular Dynamics Characterization of the Free and Encapsidated RNA2 of CCMV with the oxRNA Model.

Macromolecular rapid communications·2024
Same author

Pericapsular nerve group (PENG) block combined with local infiltration analgesia is not superior to local infiltration analgesia for the management of postoperative pain after primary elective total hip arthroplasty: A prospective, randomized, controlled, single-blind trial.

Heliyon·2024
Same journal

Detection, communication, and individual identification with deep audio embeddings: A case study with North Atlantic right whales.

PLoS computational biology·2026
Same journal

Exploring the structural lexicon of the Proteome via Metric Geometry.

PLoS computational biology·2026
Same journal

Linking retinal sampling in neural encoding models to temporal profiles of visual processing in humans.

PLoS computational biology·2026
Same journal

CAdir: Joint clustering of cells and genes for single-cell transcriptomics with visualization-driven cluster quality assessment.

PLoS computational biology·2026
Same journal

Systematic design of auxotrophic strains and media conditions to probe metabolic functions in E. coli.

PLoS computational biology·2026
Same journal

Neuronal excitability and parameter variability in the Hodgkin-Huxley model.

PLoS computational biology·2026
See all related articles

Related Experiment Video

Updated: Apr 2, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.2K

ARNy plotter: A comprehensive web server for RNA ensemble structural analysis and visualization.

Louis Meuret1, Julien Rey1,2, Samuela Pasquali1

  • 1Université Paris Cité, CNRS UMR 8251, Inserm ERL 1133, Unité de Biologie Fonctionnelle et Adaptative, Paris, France.

Plos Computational Biology
|March 31, 2026
PubMed
Summary
This summary is machine-generated.

ARny Plotter is a new web platform for analyzing RNA structural ensembles. It offers comprehensive visualization and analysis of RNA dynamics, aiding RNA structural biology research.

More Related Videos

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.4K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.3K

Related Experiment Videos

Last Updated: Apr 2, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.2K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.4K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.3K

Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • RNA molecules exhibit significant flexibility and diverse conformational landscapes, posing challenges for structural analysis.
  • Existing tools often focus on static structures or offer limited dynamic analysis capabilities.

Purpose of the Study:

  • To present ARNy Plotter, a user-friendly web platform for comprehensive analysis and visualization of RNA structural ensembles.
  • To provide an integrated environment for exploring RNA dynamics and conformational heterogeneity.

Main Methods:

  • ARny Plotter integrates multiple analysis methods including RMSD/eRMSD distributions, torsion-angle variability, dynamic secondary structures, and contact networks.
  • The platform leverages MDAnalysis, Barnaba, and foRNA for data processing and MolStar for real-time 3D visualization.
  • Supports all major trajectory and ensemble formats, with options for offline use and an API for automated figure generation.

Main Results:

  • Enables intuitive examination of various aspects of RNA structural ensembles, including conformational landscapes and population distributions.
  • Facilitates in-depth exploration of conformational transitions and dynamic patterns within RNA structures.
  • Allows for sharing of results without distributing large datasets.

Conclusions:

  • ARny Plotter addresses the need for accessible, comprehensive, and interactive tools in RNA structural biology.
  • The platform enhances the study of RNA dynamics and conformational ensembles.
  • Freely available online and supports offline use, promoting wider adoption in the research community.