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

Visualization of protein interaction networks: problems and solutions.

Giuseppe Agapito1, Pietro Hiram Guzzi, Mario Cannataro

  • 1Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Italy.

BMC Bioinformatics
|February 2, 2013
PubMed
Summary

Choosing the right protein-protein interaction network (PIN) visualization tool is challenging due to numerous options. Open-source tools like Cytoscape offer extensibility, while parallel tools like NAViGaTOR provide faster analysis of large networks.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Protein-protein interactions (PPI) form networks (PINs) crucial for understanding cellular functions.
  • Visualizing these complex networks aids in identifying substructures like protein complexes.
  • Challenges in PIN visualization include large network size and data heterogeneity.

Purpose of the Study:

  • To analyze and compare existing software tools for protein-protein interaction network (PIN) visualization.
  • To evaluate tools based on technology, interoperability, visualization capabilities, and analysis functions.
  • To guide researchers in selecting appropriate tools for their specific needs in PIN analysis.

Main Methods:

  • A systematic review of current PIN visualization software was conducted.
  • Tools were assessed based on criteria including technology (OS, license), interoperability (import/export formats), visualization features (layouts, rendering), and analytical functions.
  • Comparative analysis focused on the strengths and weaknesses of different visualization approaches.

Main Results:

  • A wide array of PIN visualization tools exist, varying in sophistication and focus.
  • Some tools excel in advanced 2D/3D visualization and layout algorithms.
  • Other tools prioritize data integration, annotation, and systems biology applications.

Conclusions:

  • Open-source, extensible tools like Cytoscape are favored for community-driven development and long-term sustainability.
  • Emerging parallel processing tools, such as NAViGaTOR, offer high interactivity and near real-time performance for large-scale network analysis.
  • The choice between open-source flexibility and parallel performance depends on specific research requirements.