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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Protein Networks02:26

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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.
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piRNA - Piwi-interacting RNAs02:57

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PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
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Related Experiment Video

Updated: Mar 22, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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NPInter v3.0: an upgraded database of noncoding RNA-associated interactions.

Yajing Hao1, Wei Wu1, Hui Li2

  • 1Key Laboratory of RNA Biology Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China University of Chinese Academy of Sciences, Beijing, 100049, China.

Database : the Journal of Biological Databases and Curation
|April 19, 2016
PubMed
Summary

The updated NPInter v3.0 database now includes over 491,000 experimentally verified interactions for noncoding RNAs (ncRNAs), particularly long noncoding RNAs (lncRNAs). This resource aids researchers in understanding ncRNA functions and interactions with other biomolecules.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Noncoding RNAs (ncRNAs) play crucial roles in gene regulation, but their functions are not fully understood.
  • A significant number of ncRNAs have been identified, necessitating comprehensive databases for functional annotation.
  • Understanding ncRNA interactions with other biomolecules is key to deciphering their biological roles.

Purpose of the Study:

  • To update and enhance the NPInter database (version 3.0) for noncoding RNA interactions.
  • To provide researchers with a more informative and organized resource for studying ncRNA functions.
  • To facilitate the prediction of ncRNA functions using curated interaction data.

Main Methods:

  • Manual curation of interactions from scientific literature and high-throughput experimental data.
  • In silico prediction of lncRNA-miRNA interactions supported by AGO CLIP-seq data.
  • Expansion and organization of the database with detailed information on tissues, cell lines, and experimental conditions.

Main Results:

  • NPInter v3.0 contains 491,416 experimentally verified interactions involving ncRNAs, including long noncoding RNAs (lncRNAs).
  • The database incorporates data from 68 experimental technologies across 188 tissues/cell lines, offering enhanced details on binding sites and conservation.
  • A high-confidence set of interactions was defined, enabling functional predictions for lncRNAs in humans and mice.

Conclusions:

  • NPInter v3.0 is a significantly expanded and improved resource for exploring noncoding RNA interactions.
  • The database facilitates a deeper understanding of ncRNA functions, particularly lncRNAs, through comprehensive, curated data.
  • Enhanced features and web services, including a genome browser, improve usability for researchers.