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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...
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...

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Related Experiment Video

Updated: Jun 12, 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

MODEVO: exploring modularity and evolution of protein interaction networks.

Michał Woźniak1, Jerzy Tiuryn, Janusz Dutkowski

  • 1Institute of Informatics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland.

Bioinformatics (Oxford, England)
|May 29, 2010
PubMed
Summary
This summary is machine-generated.

We created Cytoscape plugins to map evolving protein interaction networks. These tools help understand cell component formation by analyzing protein complexes and pathways evolutionarily.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Systems Biology

Background:

  • Understanding the evolution of cellular components requires analyzing protein complexes and pathways.
  • Existing tools may not adequately capture the dynamic, modular nature of evolving biological networks.

Purpose of the Study:

  • To develop novel computational tools for analyzing evolving protein interaction networks.
  • To provide a method for mapping and visualizing protein network evolution at the module level.

Main Methods:

  • Development of two independent Cytoscape plugins: APCluster and NetworkEvolution.
  • APCluster plugin utilizes an affinity propagation (AP) algorithm for graph clustering.
  • NetworkEvolution plugin enables visualization of modules across evolutionary stages.

Main Results:

  • Successfully created functional Cytoscape plugins for network analysis.
  • Demonstrated the capability to decompose networks into coherent modules using APCluster.
  • Enabled visualization of module evolution with NetworkEvolution.

Conclusions:

  • The developed plugins offer novel insights into the formation of basic cellular functional components.
  • Interrogating protein complexes and pathways in an evolutionary context is crucial for systems biology.
  • These tools facilitate the study of network evolution at a modular level.