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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 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,...
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,...
RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
piRNA - Piwi-interacting RNAs02:57

piRNA - Piwi-interacting RNAs

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...
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...

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Novel RNA-Binding Proteins Isolation by the RaPID Methodology
11:19

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Published on: September 30, 2016

PRD: A protein-RNA interaction database.

Shigeo Fujimori1, Katsuya Hino, Ayumu Saito

  • 1Division of Interactome Medical Sciences, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai Minato-ku, Tokyo 108-8639, Japan.

Bioinformation
|October 12, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces PRD, a new online database for protein-RNA interactions (PRIs). PRD compiles over 10,000 interactions, offering a valuable resource for studying PRI networks.

Keywords:
Biomolecular interactionDatabaseRNA binding proteinprotein-RNA interaction

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Published on: September 30, 2016

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Area of Science:

  • Molecular Biology
  • Bioinformatics

Background:

  • Protein-RNA interactions (PRIs) are crucial for cellular functions but lack comprehensive data.
  • Existing databases extensively cover protein-protein interactions, enabling network analysis.
  • Data compilation for PRIs remains limited compared to other molecular interactions.

Purpose of the Study:

  • To establish PRD, a centralized online database for protein-RNA interactions.
  • To provide a comprehensive resource for researchers studying PRIs.
  • To facilitate network-level analysis of protein-RNA interaction networks.

Main Methods:

  • Compiled PRI data from diverse sources, including scientific literature.
  • Stored over 10,000 interactions using the PSI-MI 2.5 standard.
  • Developed a web interface for browsing and searching the database.

Main Results:

  • Created PRD, an accessible online database of PRIs.
  • Integrated over 10,000 molecular interactions with gene-level data.
  • Enabled flexible keyword searches and browsing of interaction data.

Conclusions:

  • PRD serves as a vital reference for protein-RNA interactions.
  • The database is a valuable resource for understanding PRI network characteristics.
  • PRD supports further research into the roles of PRIs in cellular processes.