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

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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
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 Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

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...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
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...

You might also read

Related Articles

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

Sort by
Same author

Unraveling the degradation mechanisms of commercial cylindrical sodium-ion batteries under high cut-off voltages.

RSC advances·2026
Same author

Single-nucleus transcriptomic atlas of postnatal camel liver development identifies candidate adaptive features.

BMC genomics·2026
Same author

SHREC 2025: Protein surface shape retrieval including electrostatic potential.

Computers & graphics·2026
Same author

Treatment Patterns and Barriers to Care Among U.S. Adults With Co-Occurring Substance Use Disorder and Mental Illness.

The American journal of psychiatry·2026
Same author

Orbital-Engineered Sn/RuO<sub>2</sub> Nanocatalyst with Self-Regulating Electron Configuration for Durable Chlorine Evolution at Industrial Current Densities.

ACS applied materials & interfaces·2026
Same author

The role of macrophage-myofibroblast transition in the pathogenesis of multi-organ fibrosis.

Tissue & cell·2026

Related Experiment Video

Updated: Jun 11, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures.

Haotian Li1, Yangyu Huang1, Yi Xiao1

  • 1Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China.

Plos One
|March 31, 2017
PubMed
Summary

We developed 3dRPC-Score, a novel scoring function for predicting 3D RNA-protein complex structures. This method improves accuracy by considering pair conformations, not just distances, ensuring consistent performance across datasets.

More Related Videos

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

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

Related Experiment Videos

Last Updated: Jun 11, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

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

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

Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Predicting 3D RNA-protein complex structures is crucial for understanding molecular mechanisms.
  • Current scoring functions often rely on limited benchmarks and struggle with accuracy.
  • Scoring functions typically depend only on distance, not conformational details.

Purpose of the Study:

  • To develop an accurate and reliable scoring function for 3D RNA-protein complex structure prediction.
  • To introduce a pair-conformation-dependent scoring approach.
  • To improve upon existing distance-dependent scoring methods.

Main Methods:

  • Proposed 3dRPC-Score, a novel scoring function for RNA-protein interactions.
  • Incorporated pair-conformation dependence, assigning similar energies to similar conformations.
  • Evaluated performance using benchmark datasets for 3D structure prediction.

Main Results:

  • 3dRPC-Score demonstrates consistent performance across three independent test sets.
  • The pair-conformation-dependent approach shows improved scoring capabilities.
  • The new function addresses limitations of existing distance-only scoring methods.

Conclusions:

  • 3dRPC-Score offers a more accurate method for predicting 3D RNA-protein complex structures.
  • Conformational similarity is a key factor for improving scoring function performance.
  • This approach provides a robust tool for structural bioinformatics research.