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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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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Triangle network motifs predict complexes by complementing high-error interactomes with structural information.

Bill Andreopoulos1, Christof Winter, Dirk Labudde

  • 1Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany. williama@biotec.tu-dresden.de

BMC Bioinformatics
|June 30, 2009
PubMed
Summary
This summary is machine-generated.

Integrating protein-protein interaction networks (PPINs) with structural domain-domain interactions (SDDIs) into PPI-SDDI-PPI triangles significantly improves protein complex identification. These triangles offer a 20-fold increase in overlap with known complexes compared to traditional methods.

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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Systems Biology

Background:

  • High-throughput studies generate noisy protein-protein interaction networks (PPINs) with low inter-study overlap.
  • Second-level neighbors in PPINs have been used for protein function prediction and complex finding.
  • Structural domain-domain interactions (SDDIs) provide binding evidence on proteins.

Purpose of the Study:

  • To develop a novel method for identifying protein complexes in error-prone PPINs.
  • To assess the utility of integrating PPINs with SDDIs for complex detection.
  • To investigate the biological basis of functional similarity in protein interaction networks.

Main Methods:

  • Retrieving second-level neighbors from PPINs.
  • Complementing PPIN data with structural domain-domain interactions (SDDIs).
  • Forming PPI-SDDI-PPI triangles to represent combined interaction evidence.

Main Results:

  • PPI-SDDI-PPI triangles showed a ~20-fold higher overlap with known protein complexes (MIPS) than PPINs alone.
  • The integration of SDDIs explains the functional similarity observed between second-level neighbors in PPINs.
  • Reconstruction of myosin-actin processes demonstrated the practical utility of PPI-SDDI-PPI triangles.

Conclusions:

  • Triangles of mixed data types, particularly integrating PPINs with SDDIs, are effective for finding protein complexes in noisy networks.
  • Structural SDDIs enhance the identification of protein complexes within PPINs.
  • Limited structural information can substantially improve complex discovery in typical PPINs.