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 Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. 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) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

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...
RNA Structure01:23

RNA Structure

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...
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

You might also read

Related Articles

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

Sort by
Same author

ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment.

Nucleic acids research·2026
Same author

The Nucleic Acids Circular Dichroism and Fourier Transform Databases NACDDB and NAIRDB: New Tools for RNA Structural Analysis.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

MODOMICS: a database of RNA modifications and related information. 2025 update and 20th anniversary.

Nucleic acids research·2025
Same author

Blind prediction of complex water and ion ensembles around RNA in CASP16.

bioRxiv : the preprint server for biology·2025
Same author

Evaluation of single-template ligand-based methods for the discovery of small-molecule nucleic acid binders.

Briefings in bioinformatics·2025
Same author

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16.

Proteins·2025
Same journal

SA-MTP: a structure-aware framework for multifunctional therapeutic peptide annotation.

Briefings in bioinformatics·2026
Same journal

Genome assemblies and annotations are not static and need support for tracking their evolution.

Briefings in bioinformatics·2026
Same journal

A historical journey of metabolite-protein interaction discovery: from data harmonization to AI-driven prediction.

Briefings in bioinformatics·2026
Same journal

Bridging local-global transmembrane protein contexts with contrastive pretraining for alignment-free pathogenicity prediction.

Briefings in bioinformatics·2026
Same journal

Prediction of drug hypersensitivity by comprehensive modeling of HLA-peptidomes.

Briefings in bioinformatics·2026
Same journal

EssTFNet: integration of adaptive time-frequency and DNA language models for interpretable human essential gene prediction.

Briefings in bioinformatics·2026
See all related articles

Related Experiment Video

Updated: May 29, 2026

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

RNA tertiary structure prediction with ModeRNA.

Magdalena Rother1, Kristian Rother, Tomasz Puton

  • 1Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.

Briefings in Bioinformatics
|September 8, 2011
PubMed
Summary
This summary is machine-generated.

ModeRNA software predicts RNA structures using comparative modeling. This study details modeling Escherichia coli tRNA(Thr) for complexes with aminoacyl-tRNA synthetases, offering a valuable tool for RNA research.

More Related Videos

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

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Related Experiment Videos

Last Updated: May 29, 2026

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

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

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Noncoding RNAs play crucial roles in cellular functions.
  • RNA structure is intrinsically linked to its function.
  • Experimental RNA structure determination is often time-consuming and costly, driving the need for computational methods.

Purpose of the Study:

  • To present a detailed study on the ModeRNA software for RNA structure prediction.
  • To guide users through the process of modeling specific RNA structures, exemplified by Escherichia coli tRNA(Thr).
  • To explore different modeling strategies within the ModeRNA framework.

Main Methods:

  • Utilizing the ModeRNA software, which employs a comparative modeling approach.
  • Selecting appropriate structural templates and performing sequence alignments.
  • Applying and evaluating three distinct modeling strategies for tRNA(Thr).

Main Results:

  • Successful modeling of Escherichia coli tRNA(Thr) in a conformation relevant to aminoacyl-tRNA synthetase complex formation.
  • Evaluation of generated models using six independent benchmarks.
  • Demonstration of ModeRNA's capability for accurate RNA structure prediction.

Conclusions:

  • ModeRNA is a viable tool for RNA structure prediction when template structures and alignments are available.
  • The study provides a practical workflow for modeling RNA structures with ModeRNA.
  • ModeRNA offers a valuable, accessible resource for researchers in RNA biology.