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Protein Networks

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 Interfaces

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...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

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Updated: Mar 10, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

PROPER: global protein interaction network alignment through percolation matching.

Ehsan Kazemi¹, Hamed Hassani², Matthias Grossglauser³

¹School of Computer and Communication Sciences, EPFL, Lausanne, Switzerland. ehsan.kazemi@epfl.ch.

BMC Bioinformatics

|December 14, 2016

Summary

This summary is machine-generated.

PROPER is a new protein-protein interaction network alignment algorithm. It accurately and quickly identifies conserved biological pathways across species, improving biological knowledge transfer.

Keywords:

Biological network Global network alignment Percolation graph matching Protein-protein interaction

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Area of Science:

Bioinformatics
Computational Biology
Systems Biology

Background:

Protein-protein interaction (PPI) network alignment is crucial for understanding inter-species relationships and transferring biological knowledge.
Existing PPI network alignment algorithms face challenges in achieving both accuracy and scalability.
Accurate alignment requires high biological and structural similarity detection.

Purpose of the Study:

Introduce PROPER, a novel global network alignment algorithm for PPI networks.
Evaluate PROPER's accuracy and speed compared to existing methods.
Demonstrate PROPER's capability in detecting conserved biological pathways.

Main Methods:

Developed a new global network alignment algorithm named PROPER.
Tested PROPER on real PPI datasets and synthetic networks.
Utilized a parsimonious evolutionary model for performance analysis.

Main Results:

PROPER demonstrates superior accuracy and speed compared to other global network alignment methods.
The algorithm effectively identifies significant conserved biological pathways between species.
Performance analysis using an evolutionary model explains PROPER's effectiveness.

Conclusions:

PROPER shows high potential for applications including biological pathway detection, protein complex identification, and PPI prediction.
The PROPER algorithm offers advancements in cross-species biological network analysis.
PROPER is publicly available for further research and application.