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Related Concept Videos

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 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,...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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

Published on: March 3, 2015

Efficient and accurate Greedy Search Methods for mining functional modules in protein interaction networks.

Jieyue He1, Chaojun Li, Baoliu Ye

  • 1School of Computer Science and Engineering, Key Lab of Computer Network & Information Integration, MOE, Southeast University, Nanjing, 210018, China. jieyuehe@seu.edu.cn

BMC Bioinformatics
|July 5, 2012
PubMed
Summary

A new algorithm, Greedy Search Method based on Fast Clustering (GSM-FC), efficiently detects protein complexes in protein-protein interaction networks. This method accurately identifies functional modules while significantly reducing computational time.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Protein-protein interaction (PPI) networks are crucial for understanding cellular functions.
  • Existing algorithms for detecting protein complexes often overlook inherent structural organization and are computationally intensive.
  • Experimentally validated protein complexes frequently exhibit core/attachment structures.

Purpose of the Study:

  • To develop an efficient computational method for identifying protein complexes within PPI networks.
  • To address the limitations of existing algorithms in terms of computational cost and consideration of structural organization.

Main Methods:

  • Proposed the Greedy Search Method based on Core-Attachment structure (GSM-CA) to detect protein modules based on edge weights and core/attachment node criteria.
  • Introduced the Greedy Search Method based on Fast Clustering (GSM-FC) to optimize computational speed by traversing edges once.
  • The GSM-FC method utilizes a greedy procedure for efficient module separation.

Main Results:

  • Applied GSM-CA and GSM-FC to the *Saccharomyces cerevisiae* PPI network.
  • Detected numerous significant functional modules, with high concordance to known protein complexes.
  • GSM-FC demonstrated superior speed and accuracy compared to existing competing algorithms.

Conclusions:

  • The proposed GSM-FC algorithm effectively identifies statistically significant protein modules using a novel edge weight definition and greedy search.
  • The algorithm significantly reduces computational time while maintaining high prediction accuracy.
  • This approach offers an efficient and accurate method for protein complex detection in large-scale PPI networks.