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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...

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Related Experiment Video

Updated: Sep 22, 2025

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

ProMoCell and ProModb: Web services for analyzing interaction-based functionally localized protein modules in a cell.

Barnali Das¹, Pralay Mitra²

¹Department of Computer Science and Engineering, Indian Institute of Technology, Kharagpur, 721302, West Bengal, India.

Journal of Molecular Modeling

|May 25, 2022

Summary

This summary is machine-generated.

We developed ProMoCell and ProModb to identify cellular functional modules using protein interaction networks. These tools aid in understanding cell biology and disease, advancing modular pharmacology.

Keywords:

Functional modules Markov cluster algorithm Protein interaction networks Protein locality graph Spatial localization

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Last Updated: Sep 22, 2025

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

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Published on: March 3, 2015

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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

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

Published on: October 19, 2021

Area of Science:

Systems Biology
Bioinformatics
Computational Biology

Background:

Cellular organization is understood through interaction networks, revealing cooperation among functional modules.
Identifying cellular functional modules enhances understanding of biological networks and evolutionary signals.

Purpose of the Study:

To develop ProMoCell for real-time web scraping and clustering of cellular functional units.
To create ProModb, a database of precomputed functional modules based on protein-protein interaction networks.
To provide an integrated web service synchronized with KEGG pathways for generating organism-specific protein modules.

Main Methods:

ProMoCell performs real-time web scraping to gather experimental data from online sources.
Protein Locality Graphs are constructed to cluster cellular functional units.
ProModb houses precomputed functional modules, synchronized with the KEGG pathway database.

Main Results:

ProMoCell successfully generates clusters of cellular functional units.
ProModb offers a database of whole-cell, network-based functional modules.
The web service allows generation of spatially localized protein modules for any KEGG organism.

Conclusions:

ProMoCell and ProModb provide a comprehensive tool for analyzing spatial locality-based protein modules.
These services are valuable for modular pharmacology in disease diagnosis, prevention, and treatment.
The integrated approach aids in understanding cellular function and evolutionary insights.