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

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
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...
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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

You might also read

Related Articles

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

Sort by
Same author

DynamiCare: A Dynamic Multi-Agent Framework for Interactive and Open-Ended Medical Decision-Making.

AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science·2026
Same author

Machine learning identifies clinical and sociodemographic factors contributing to post-COVID hospitalization and cardiovascular risk in patients with peripheral artery disease.

Scientific reports·2025
Same author

Genetic Analysis of Recently Discovered Least Chub Populations in the Upper Snake River and Bonneville Drainages.

Ecology and evolution·2025
Same author

DGX: Uncovering General Behavior of Deep Graph Models With Model-Level Explanation.

IEEE transactions on computational biology and bioinformatics·2025
Same author

Study Preregistration: Data-Driven Profiles of Youth Executive Function and Their Longitudinal Associations With Externalizing Problems.

Journal of the American Academy of Child and Adolescent Psychiatry·2025
Same author

Can machine learning predict late seizures after intracerebral hemorrhages? Evidence from real-world data.

Epilepsy & behavior : E&B·2024
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: Jun 6, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

PRIDB: a Protein-RNA interface database.

Benjamin A Lewis1, Rasna R Walia, Michael Terribilini

  • 1Bioinformatics and Computational Biology Program, Iowa State University, Iowa, USA. balewis@iastate.edu

Nucleic Acids Research
|November 13, 2010
PubMed
Summary
This summary is machine-generated.

The Protein-RNA Interface Database (PRIDB) offers a comprehensive resource for analyzing protein-RNA interactions. It provides tools for detailed studies and automated data set generation for machine learning applications.

More Related Videos

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Related Experiment Videos

Last Updated: Jun 6, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Protein-RNA interactions are crucial for numerous biological processes.
  • Analyzing these interfaces is essential for understanding molecular mechanisms.
  • Existing resources may lack comprehensive data or user-friendly analysis tools.

Purpose of the Study:

  • To introduce the Protein-RNA Interface Database (PRIDB) as a centralized resource.
  • To facilitate detailed analysis of protein-RNA complexes and their interfaces.
  • To enable automated data set generation for statistical and machine learning applications.

Main Methods:

  • Extraction of protein-RNA interfaces from the Protein Data Bank (PDB).
  • Development of tools for rapid display of interfacial amino acids and ribonucleotides.
  • Integration of motif identification (ProSite, FR3D) and 3D visualization (Jmol).

Main Results:

  • PRIDB currently contains structural information for 926 protein-RNA complexes.
  • Provides atomic- and residue-level contact information downloadable in a machine-readable format.
  • Offers several non-redundant benchmark data sets for research.

Conclusions:

  • PRIDB serves as a valuable, freely accessible resource for researchers studying protein-RNA interactions.
  • The database supports diverse analyses, from individual complex investigations to large-scale computational studies.
  • Facilitates advancements in understanding the structural and functional roles of protein-RNA complexes.