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Related Concept Videos

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,...
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...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Related Experiment Video

Updated: May 24, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Published on: March 3, 2015

Analyzing protein-protein interaction networks.

Gavin C K W Koh1, Pablo Porras, Bruno Aranda

  • 1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

Journal of Proteome Research
|March 6, 2012
PubMed
Summary
This summary is machine-generated.

This tutorial guides researchers on analyzing molecular interaction networks. It demonstrates building, visualizing, and interpreting protein-protein interaction data using IntAct and Cytoscape for biological discovery.

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Last Updated: May 24, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
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Published on: March 3, 2015

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Published on: August 21, 2019

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Area of Science:

  • Systems Biology
  • Bioinformatics
  • Proteomics

Background:

  • The "omics" era presents challenges in biological research, necessitating new analytical strategies.
  • Molecular interaction networks offer insights into cellular processes but are complex to interpret.
  • Limitations in interaction detection methods and data completeness require careful data utilization.

Purpose of the Study:

  • To provide an overview of key considerations for researchers working with molecular interaction datasets.
  • To outline a practical example of interactome analysis.
  • To demonstrate the process of building, visualizing, and analyzing protein-protein interaction networks.

Main Methods:

  • Utilized the IntAct molecular interaction database.
  • Employed the Cytoscape software platform and its plugins (BiNGO, clusterMaker).
  • Started with a protein list from a mass spectrometry-based proteomics experiment.

Main Results:

  • Successfully demonstrated the construction of a protein-protein interaction network.
  • Visualized the complex network structure for easier interpretation.
  • Applied analysis techniques to derive biological insights from the network.

Conclusions:

  • Researchers can effectively analyze molecular interaction data using available databases and software.
  • This approach facilitates the interpretation of complex biological networks.
  • The tutorial provides a practical workflow for interactome analysis in biological research.