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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,...
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...

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Mapping Dysfunctional Protein-Protein Interactions in Disease
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IDDI: integrated domain-domain interaction and protein interaction analysis system.

Yul Kim1, Bumki Min1, Gwan-Su Yi1

  • 1Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, South Korea.

Proteome Science
|July 5, 2012
PubMed
Summary

We developed IDDI, a system integrating protein-protein and domain-domain interactions (PPIs and DDIs). IDDI enhances DDI analysis with a novel scoring system and a unified interface for exploring interaction networks.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein-protein interactions (PPIs) are crucial for understanding protein function.
  • Domain-domain interactions (DDIs) provide detailed insights into binding mechanisms.
  • Existing DDI resources are fragmented and lack standardized performance evaluation.

Purpose of the Study:

  • To create a comprehensive and organized system for analyzing protein-protein and domain-domain interactions.
  • To develop a novel scoring scheme for assessing the reliability of predicted domain-domain interactions.
  • To integrate diverse DDI data with protein-protein interaction information for a unified analysis.

Main Methods:

  • Integrated three structure-based and twenty computationally predicted DDI datasets.
  • Developed a novel scoring scheme considering prediction scores, method confidence, and dataset independencies.
  • Constructed the IDDI system with a unified interface for exploring protein and domain interaction networks.

Main Results:

  • IDDI currently provides 204,705 DDIs across 7,351 Pfam domains, an eightfold increase.
  • 50.4% of PPIs are now correlated with DDIs, more than double previous resources.
  • The new scoring scheme demonstrated superior accuracy compared to existing methods.

Conclusions:

  • IDDI offers a significantly expanded and more reliable resource for DDI analysis.
  • The system facilitates a comprehensive understanding of protein interactions at both protein and domain levels.
  • IDDI is freely accessible, promoting further research in protein interaction networks.