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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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Related Experiment Video

Updated: May 14, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

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

Published on: October 19, 2021

SPINAL: scalable protein interaction network alignment.

Ahmet E Aladag1, Cesim Erten

  • 1Department of Computer Engineering, Bogaziçi University, Bebek, Istanbul 34342, Turkey.

Bioinformatics (Oxford, England)
|February 16, 2013
PubMed
Summary

We developed SPINAL, a novel heuristic algorithm for protein-protein interaction network alignment. SPINAL accurately identifies functionally orthologous proteins and outperforms existing methods in comparative systems biology.

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Last Updated: May 14, 2026

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

Published on: October 19, 2021

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Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling
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Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Systems Biology

Background:

  • Protein-protein interaction (PPI) networks are crucial for understanding cellular processes.
  • Pairwise global alignment of PPI networks aims to map proteins between species to infer functional orthologs.
  • Accurate mapping is essential for comparative systems biology, including function prediction and evolutionary analysis.

Purpose of the Study:

  • To address the computational complexity of protein-protein interaction network alignment.
  • To develop an accurate and scalable algorithm for identifying functionally orthologous proteins across species.
  • To improve comparative systems biology analyses through reliable network alignment.

Main Methods:

  • Introduced SPINAL, a polynomial-time heuristic algorithm for pairwise global network alignment.
  • Employed a two-phase approach: coarse-grained alignment using local neighborhood matching and fine-grained alignment via iterative improvement.
  • Utilized neighborhood bipartite graphs and contributors as core components in both alignment phases.

Main Results:

  • Demonstrated that protein-protein interaction network alignment is NP-hard, even for simple network structures.
  • SPINAL achieved superior accuracy compared to state-of-the-art algorithms on yeast, fly, human, and worm PPI networks.
  • The algorithm exhibits excellent scalability, providing accurate results within reasonable computation times.

Conclusions:

  • SPINAL offers a significant advancement in protein-protein interaction network alignment.
  • The method provides a robust tool for identifying functionally orthologous proteins, enhancing comparative systems biology research.
  • Open-source code and data are available, facilitating reproducibility and further development.