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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 Networks

Protein Networks

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...

Protein-Protein Interfaces

Protein-Protein Interfaces

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...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

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Related Experiment Video

Updated: Apr 25, 2026

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

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

Published on: March 3, 2015

Alignment-free protein interaction network comparison.

Waqar Ali¹, Tiago Rito¹, Gesine Reinert¹

¹Department of Statistics, University of Oxford, Oxford OX1 3TG, UK and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, CA 90089-2910, USA.

Bioinformatics (Oxford, England)

|August 28, 2014

Summary

This summary is machine-generated.

Netdis, a novel topology-based distance measure, enables accurate phylogenetic reconstruction from biological networks. This method overcomes limitations of traditional network alignment, revealing evolutionary insights from network topology.

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Area of Science:

Computational Biology
Bioinformatics
Systems Biology

Background:

Current biological network comparison methods, primarily network alignment, struggle with incomplete and error-prone data.
Network alignment results are often unsuitable for distance-based evolutionary analyses.
Existing approaches fail to fully leverage network topology for evolutionary insights.

Purpose of the Study:

To introduce Netdis, a topology-based distance measure for biological networks.
To enable network phylogeny reconstruction and distance-based evolutionary analysis.
To demonstrate the utility of network topology in understanding evolutionary processes.

Main Methods:

Developed Netdis, a novel algorithm measuring distances between networks based on topology.
Validated Netdis on random graph models to assess its independence from network size and density.
Applied Netdis to protein-interaction networks for phylogenetic tree reconstruction.

Main Results:

Netdis successfully distinguishes between different random graph models.
Phylogenetic trees of species were accurately reconstructed using only protein interaction network topology.
Netdis demonstrated speed and simplicity, clustering diverse biological and non-biological networks by type.

Conclusions:

Protein interaction network topology contains significant evolutionary information, independent of individual interaction conservation.
Netdis provides a robust and efficient tool for network comparison and phylogenetic analysis.
The method's applicability extends beyond biological networks, facilitating broader network classification.