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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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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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Detecting protein complexes in a PPI network: a gene ontology based multi-objective evolutionary approach.

Anirban Mukhopadhyay1, Sumanta Ray, Moumita De

  • 1Department of Computer Science and Engineering, University of Kalyani, Kalyani, India. anirban@klyuniv.ac.in

Molecular Biosystems
|September 20, 2012
PubMed
Summary

We developed PROCOMOSS, an algorithm that identifies protein complexes in protein-protein interaction networks by combining network structure and biological function. This method aids in understanding cellular mechanisms and disease-related gene modules.

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Area of Science:

  • Computational Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Protein complexes are crucial for cellular functions.
  • Identifying these complexes in protein-protein interaction (PPI) networks is key to understanding cellular organization and dynamics.
  • High-throughput techniques generate extensive PPI data, enabling computational prediction of protein complexes.

Purpose of the Study:

  • To develop and present PROCOMOSS, a novel algorithm for detecting protein complexes within PPI networks.
  • To integrate both network topology and biological functional similarity for improved complex prediction.
  • To validate the algorithm's performance on biological datasets and demonstrate its applicability to disease-related networks.

Main Methods:

  • PROCOMOSS utilizes a multi-objective evolutionary approach to partition PPI networks into clusters representing protein complexes.
  • The algorithm incorporates objective functions based on network graphical properties and Gene Ontology (GO) semantic similarity.
  • Three distinct GO semantic similarity measures are employed to group functionally related proteins.

Main Results:

  • PROCOMOSS was applied to two Saccharomyces cerevisiae PPI datasets, successfully identifying predicted protein complexes.
  • The algorithm was also applied to a human PPI network associated with gastric cancer, demonstrating real-world applicability.
  • Gene Ontology and pathway analyses confirmed the biological significance of the identified gene modules.

Conclusions:

  • PROCOMOSS effectively predicts protein complexes by integrating network structure and functional similarity.
  • The algorithm provides a valuable tool for dissecting cellular mechanisms and identifying disease-associated biological modules.
  • This approach enhances our ability to interpret complex biological networks and their functional implications.