Jove
Visualize
Contact Us

Related Concept Videos

Nucleic Acid Structure01:25

Nucleic Acid Structure

6.3K
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...
6.3K
RNA Stability01:53

RNA Stability

33.8K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
33.8K
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

10.2K
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...
10.2K
Conserved Binding Sites01:49

Conserved Binding Sites

4.3K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.3K

You might also read

Related Articles

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

Sort by
Same author

TriRNASP: A knowledge-based potential with three-body effects for accurate RNA structure evaluation.

Biophysical journal·2026
Same author

A review of recent advances in generative artificial intelligence models for biomolecular sciences.

Acta pharmaceutica Sinica. B·2026
Same author

R3J-AGNN: GNN-Based Prediction of Inter-Branch Angles in RNA Three-Way Junctions from Secondary Structure.

Biology·2026
Same author

Unexpected Applications of AlphaFold in Molecular Sciences.

Annual review of biochemistry·2026
Same author

gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure.

Biomolecules·2026
Same author

Inorganic High-Performance Fiber-Based Materials for Electromagnetic Interference Shielding: Fundamentals, Fabrications, and Emerging Applications.

Nano-micro letters·2026
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: Aug 7, 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

cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation.

Ya-Lan Tan1,2, Xunxun Wang2, Shixiong Yu2

  • 1Research Center of Nonlinear Science, School of Mathematical and Physical Sciences, Wuhan Textile University, Wuhan 430073, China.

NAR Genomics and Bioinformatics
|March 7, 2023
PubMed
Summary

We developed cgRNASP, a new coarse-grained statistical potential for evaluating RNA 3D structures. It offers efficient and comparable performance to all-atom methods, excelling on realistic datasets.

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
Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA
08:17

Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA

Published on: July 9, 2021

4.8K

Related Experiment Videos

Last Updated: Aug 7, 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
Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA
08:17

Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA

Published on: July 9, 2021

4.8K

Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Knowledge-based statistical potentials are crucial for RNA 3D structure prediction and evaluation.
  • Existing coarse-grained (CG) models lack reliable statistical potentials for efficient RNA structure evaluation.

Purpose of the Study:

  • To develop novel residue-separation-based CG statistical potentials for RNA 3D structure evaluation.
  • To assess the performance and efficiency of these new potentials compared to existing methods.

Main Methods:

  • Developed a series of CG statistical potentials (cgRNASP) based on residue separation at various CG levels.
  • Incorporated long-ranged and short-ranged interactions, with CG short-ranged interactions modeled more subtly than in all-atom potentials.
  • Evaluated cgRNASP against all-atom potentials (rsRNASP) and neural network-based functions using diverse test datasets, including RNA-Puzzles.

Main Results:

  • cgRNASP performance varies with CG levels but shows comparable results to rsRNASP across many datasets.
  • cgRNASP demonstrates slightly superior performance on the RNA-Puzzles dataset.
  • cgRNASP is significantly more efficient than all-atom potentials and outperforms other neural network-based functions on RNA-Puzzles.

Conclusions:

  • cgRNASP provides an efficient and effective tool for RNA 3D structure evaluation.
  • The developed CG potentials offer a promising alternative to computationally expensive all-atom methods for RNA structure analysis.