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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,...
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

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

Published on: March 3, 2015

PINA v2.0: mining interactome modules.

Mark J Cowley1, Mark Pinese, Karin S Kassahn

  • 1Cancer Research Program, Peter Wills Bioinformatics Centre, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.

Nucleic Acids Research
|November 10, 2011
PubMed
Summary
This summary is machine-generated.

The Protein Interaction Network Analysis (PINA) platform offers a unified database and tools for studying protein-protein interactions. Version 2.0 enhances network analysis with identified modules and enrichment tools for six model organisms.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Protein-protein interactions (PPIs) are fundamental to cellular processes.
  • Analyzing PPIs at a network level is crucial for understanding complex biological systems.
  • Existing resources often lack comprehensive integration and advanced analytical tools.

Purpose of the Study:

  • To present the enhanced Protein Interaction Network Analysis (PINA) platform, version 2.0.
  • To provide an integrated database and advanced tools for network-level PPI analysis.
  • To facilitate the identification and functional annotation of protein interaction modules.

Main Methods:

  • Integrated PPI data from six manually curated public databases.
  • Applied various clustering approaches to identify interaction modules within the interactome of six model organisms.
  • Annotated modules with Gene Ontology terms, KEGG pathways, Pfam domains, and MSigDB perturbations.
  • Developed a new tool for module enrichment analysis.

Main Results:

  • PINA v2.0 offers a unified PPI database with enhanced network analysis capabilities.
  • Multiple collections of protein interaction modules identified across six model organisms.
  • Comprehensive functional annotations (GO, KEGG, Pfam) provided for all identified modules.
  • A new module enrichment analysis tool is available.

Conclusions:

  • PINA v2.0 significantly enhances the study of protein interaction networks.
  • The platform provides valuable resources for systems biology research.
  • Facilitates deeper insights into cellular mechanisms through network and module analysis.