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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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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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STRING v9.1: protein-protein interaction networks, with increased coverage and integration.

Andrea Franceschini1, Damian Szklarczyk, Sune Frankild

  • 1Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland.

Nucleic Acids Research
|December 4, 2012
PubMed
Summary

The STRING database provides a global view of protein-protein interactions across many organisms. Version 9.1 enhances data mining, improves cross-species interaction transfer, and adds functional enrichment statistics.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Systems Biology

Background:

  • Understanding cellular mechanisms requires comprehensive knowledge of protein interactions.
  • Existing resources offer varying levels of detail for protein associations.
  • A global perspective integrating diverse data, including predictions, is valuable.

Purpose of the Study:

  • To describe updates to the STRING database (version 9.1).
  • To provide a comprehensive resource for protein-protein interaction data.
  • To enhance the utility of STRING for biological research.

Main Methods:

  • Automated text mining extended to full-text scientific articles for interaction data.
  • Redesigned algorithm for transferring interaction information between model organisms.
  • Integration of known and predicted protein associations with confidence scores.

Main Results:

  • STRING version 9.1 covers over 1100 organisms with integrated protein interaction networks.
  • Enhanced text mining captures more interaction information.
  • Improved cross-species transfer and statistical enrichment analysis tools.

Conclusions:

  • STRING database provides a valuable, updated resource for exploring protein-protein interactions.
  • The enhancements facilitate a more comprehensive understanding of cellular functions.
  • STRING aids researchers in analyzing biological networks and functional enrichment.