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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
08:38

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

Published on: March 3, 2015

Modularity detection in protein-protein interaction networks.

Tejaswini Narayanan1, Merril Gersten, Shankar Subramaniam

  • 1Department of Bioengineering, University of California, San Diego, USA. shankar@ucsd.edu.

BMC Research Notes
|December 31, 2011
PubMed
Summary
This summary is machine-generated.

We developed an optimized algorithm for detecting modules in biological networks, significantly reducing computation time for large datasets like protein-protein interaction networks while maintaining high-quality results.

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

  • Computational Biology
  • Network Science
  • Bioinformatics

Background:

  • Biological networks, such as protein-protein interaction networks, exhibit modularity crucial for biomolecule function and structure.
  • The Newman-Girvan (NG) algorithm is a common method for modularity detection, but its computational cost is high for large networks.
  • The NG algorithm iteratively removes edges based on betweenness centrality, generating a dendrogram for module extraction using the modularity metric (Q).

Purpose of the Study:

  • To present a novel optimization for the Newman-Girvan modularity detection algorithm.
  • To introduce an efficient termination criterion based on a target edge betweenness value.
  • To reduce the computational expense of modularity detection in large biological networks.

Main Methods:

  • Developed an optimized modularity detection algorithm with an efficient termination criterion.
  • Applied a target edge betweenness value to guide the iterative edge removal process.
  • Utilized holistic measures of graph centrality to efficiently guide modularity detection.

Main Results:

  • The optimized algorithm demonstrated significant computational gains in runtime compared to the standard NG algorithm.
  • Applied to real-world protein-protein interaction networks (Yeast, C. elegans, Drosophila), the algorithm showed consistent runtime reductions.
  • Modules detected by the optimized algorithm were qualitatively and quantitatively comparable to those from the NG algorithm, validated by metrics like modularity Q and Jaccard Similarity.

Conclusions:

  • Presented an optimized approach for efficient modularity detection in biological networks.
  • The method leverages graph centrality measures to guide the detection process effectively.
  • Empirical evaluation on large-scale biological networks confirmed significant savings in computational time with maintained module quality.