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

71.7K
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...
71.7K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

3.8K
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...
3.8K
RNA-seq03:21

RNA-seq

10.1K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.1K
Nucleic Acid Structure01:25

Nucleic Acid Structure

6.2K
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...
6.2K

You might also read

Related Articles

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

Sort by
Same author

DivideFold+: an AI-based tool for RNA secondary structure prediction with subdomains identification and visualization and data augmentation.

Journal of molecular biology·2026
Same author

Multigenerational effects of uranium exposure reveal stronger testicular dysregulation in the second generation.

Current research in toxicology·2026
Same author

Semi-supervised segmentation of RNA 3D structures using density-based clustering.

Computational and structural biotechnology journal·2026
Same author

RNAdvisor 2: A unified platform for RNA 3D model quality assessment using metrics, scoring functions, and meta-metrics.

Scientific reports·2025
Same author

A divide-and-conquer approach based on deep learning for long RNA secondary structure prediction: Focus on pseudoknots identification.

PloS one·2025
Same author

MMnc: multi-modal interpretable representation for non-coding RNA classification and class annotation.

Bioinformatics (Oxford, England)·2025
Same journal

STED: flexible cross-modal topic modeling infers cell-type-specific regulatory landscapes from bulk epigenomics.

Briefings in bioinformatics·2026
Same journal

A knowledge-guided deep learning framework for quantitative nucleic acid testing.

Briefings in bioinformatics·2026
Same journal

Optimal transport for label transfer in single-cell multi-omics integration.

Briefings in bioinformatics·2026
Same journal

Continuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity.

Briefings in bioinformatics·2026
Same journal

Evaluating completeness, coherence, and consistency of genome-scale function annotations.

Briefings in bioinformatics·2026
Same journal

Transformers for single-cell RNA sequencing: a survey.

Briefings in bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Jul 26, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.6K

C-RCPred: a multi-objective algorithm for interactive secondary structure prediction of RNA complexes integrating

Mandy Ibéné1, Audrey Legendre1, Guillaume Postic1

  • 1Université Paris-Saclay, Univ Evry, IBISC, 91020, Evry-Courcouronnes, France.

Briefings in Bioinformatics
|June 20, 2023
PubMed
Summary
This summary is machine-generated.

Predicting RNA complex structures is challenging. A new tool, C-RCPRed, uses user knowledge and probing data with a multi-objective algorithm to improve predictions for multi-RNA complexes.

Keywords:
Multi-objective algorithmRNA complexesRNA structure predictionShape data

More Related Videos

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.3K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.8K

Related Experiment Videos

Last Updated: Jul 26, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.6K
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.3K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.8K

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • RNA molecules interact with various environmental factors like ions, proteins, and other RNAs to form complexes with crucial biological functions.
  • Predicting the structure of these RNA complexes, especially those involving multiple interacting RNAs, is a significant challenge in molecular biology.

Purpose of the Study:

  • To develop and evaluate a computational tool for predicting the secondary structure of RNA complexes composed of more than two interacting RNA molecules.
  • To investigate the utility of incorporating existing knowledge about individual RNAs and experimental probing data into the structure prediction process.

Main Methods:

  • Development of C-RCPRed, an interactive tool employing a multi-objective optimization algorithm.
  • Integration of user-provided knowledge and probing data (experimental or artificial) into the prediction workflow.
  • Extensive benchmarking against state-of-the-art methods to assess prediction efficiency.

Main Results:

  • Demonstration of the effectiveness of the multi-objective optimization approach for RNA complex structure prediction.
  • Quantification of the positive impact of incorporating user knowledge and probing data on prediction accuracy.
  • Validation of C-RCPRed's performance through comprehensive benchmarking.

Conclusions:

  • The C-RCPRed tool enhances the prediction of multi-RNA complex secondary structures by leveraging user knowledge and probing data.
  • Multi-objective optimization is an efficient strategy for tackling complex RNA structure prediction problems.
  • C-RCPRed is available as an open-source program and web server, facilitating broader research in RNA structural biology.