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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

Ligand Binding and Linkage

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

Ligand Binding and Linkage

Ligand Binding and Linkage

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Updated: Mar 15, 2026

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

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

Published on: October 7, 2021

ModuleAlign: module-based global alignment of protein-protein interaction networks.

Somaye Hashemifar¹, Jianzhu Ma¹, Hammad Naveed¹

¹Toyota Technological Institute at Chicago, Chicago, IL 60637, USA.

Bioinformatics (Oxford, England)

|September 3, 2016

Summary

This summary is machine-generated.

ModuleAlign is a new algorithm for aligning protein-protein interaction networks. It improves accuracy by using local network structure, aiding in the discovery of conserved genes and pathways.

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Area of Science:

Bioinformatics
Computational Biology
Systems Biology

Background:

Protein-protein interaction (PPI) data is rapidly expanding, necessitating advanced computational interpretation.
Global network alignment is crucial for identifying conserved subnetworks, evolutionary paths, and functional orthologs across species.
Existing global network alignment methods often lack sufficient topological and functional consistency.

Purpose of the Study:

To introduce ModuleAlign, a novel global network alignment algorithm.
To enhance the accuracy and functional consistency of network alignments.
To identify conserved genes and pathways targeted by pathogens.

Main Methods:

ModuleAlign utilizes local topology information to compute a module-based homology score.
The algorithm employs hierarchical clustering of functionally related proteins within modules.
A novel iterative scheme is used to align two networks based on these modules.

Main Results:

ModuleAlign demonstrates superior performance compared to state-of-the-art methods in producing functionally consistent alignments.
The algorithm successfully identified a novel set of conserved human genes targeted by pathogens.
Alignments generated by ModuleAlign provide insights into conserved subnetworks and evolutionary relationships.

Conclusions:

ModuleAlign offers a significant advancement in global network alignment, prioritizing functional consistency.
The method facilitates the discovery of biologically relevant conserved elements between species.
This approach has implications for understanding host-pathogen interactions and identifying therapeutic targets.