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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

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Published on: March 3, 2015

A core-attachment based method to detect protein complexes in PPI networks.

Min Wu1, Xiaoli Li, Chee-Keong Kwoh

  • 1School of Computer Engineering, Nanyang Technological University, Singapore. wumi0002@ntu.edu.sg

BMC Bioinformatics
|June 3, 2009
PubMed
Summary

Detecting protein complexes is crucial. The novel COACH method identifies protein complexes by first finding core structures and then adding attachments, improving accuracy and biological relevance in protein-protein interaction networks.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Systems Biology

Background:

  • Protein complex detection is vital in the post-genomic era.
  • Existing methods often overlook the internal organization of protein complexes.
  • Protein-protein interaction (PPI) networks offer a basis for complex identification.

Purpose of the Study:

  • To introduce a novel core-attachment based method (COACH) for protein complex detection.
  • To provide insights into the inherent organization within protein complexes.
  • To improve the accuracy and biological meaningfulness of identified protein complexes.

Main Methods:

  • A two-stage approach: first identifying protein-complex cores, then incorporating attachments.
  • Evaluation through comparison with existing techniques using benchmark complexes.
  • Validation of core-attachment structures using biological evidence and knowledge.

Main Results:

  • The COACH method demonstrates superior performance compared to state-of-the-art techniques on yeast PPI networks.
  • Identified protein complexes exhibit well-matched core-attachment structures with existing biological knowledge.
  • The method provides deeper insights into protein complex organization.

Conclusions:

  • The COACH method significantly outperforms existing techniques for protein complex detection.
  • The core-attachment structures identified by COACH align well with biological understanding.
  • This approach offers valuable insights for future biological studies of protein complexes.