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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 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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NetAligner--a network alignment server to compare complexes, pathways and whole interactomes.

Roland A Pache1, Arnaud Céol, Patrick Aloy

  • 1Institute for Research in Biomedicine (IRB) Barcelona, Department of Structural and Computational Biology, Joint IRB-BSC Program in Computational Biology, c/Baldiri Reixac 10-12, 08028 Barcelona, Spain.

Nucleic Acids Research
|May 24, 2012
PubMed
Summary
This summary is machine-generated.

NetAligner is a new bioinformatics tool that identifies conserved protein complexes and pathways across species. It helps understand how interaction networks evolve by predicting missing links and assessing statistical significance.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Genome sequencing initiatives provide molecular components but not their functional interactions.
  • Thousands of gene product interrelationships require advanced bioinformatics for analysis.
  • Understanding emergent properties of biological networks is crucial.

Purpose of the Study:

  • To introduce NetAligner, a novel network alignment tool.
  • To identify conserved protein complexes and pathways across different organisms.
  • To provide insights into the evolution of biological interaction networks.

Main Methods:

  • Developed NetAligner, a network alignment tool.
  • Incorporated prediction of conserved interactions based on evolutionary distances.
  • Implemented fast statistical significance assessment for alignment solutions.
  • Created a web server for complex, pathway, and interactome-to-interactome alignments.

Main Results:

  • NetAligner enables identification of conserved protein complexes and pathways.
  • The tool predicts likely conserved interactions to address missing data in interactomes.
  • It offers fast statistical assessment, improving performance over existing methods.
  • A web server supports alignments for seven model organisms (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, Escherichia coli).

Conclusions:

  • NetAligner is a valuable tool for comparative interactomics and evolutionary network analysis.
  • The web server facilitates the study of conserved biological networks across species.
  • It aids in understanding the evolution of protein complexes and pathways.