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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

Protein Complexes with Interchangeable Parts

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...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

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Related Experiment Video

Updated: Apr 21, 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

ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis.

Daniel V Veres¹, Dávid M Gyurkó¹, Benedek Thaler²

¹Department of Medical Chemistry, Semmelweis University, Budapest, Hungary.

Nucleic Acids Research

|October 29, 2014

Summary

This summary is machine-generated.

ComPPI is a new database for protein interactions within cellular compartments. It helps filter unlikely interactions and predict functions, aiding biological research and drug design.

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Published on: June 15, 2018

Area of Science:

Bioinformatics
Molecular Biology
Network Science

Background:

Protein-protein interactions (PPIs) are crucial for cellular functions.
Understanding PPIs within specific subcellular compartments is essential for biological insight.
Existing databases often lack detailed compartmental information.

Purpose of the Study:

To introduce ComPPI, a novel database for cellular compartment-specific protein-protein interactions.
To enable compartmentalized network analysis and prediction of novel biological functions.
To provide confidence scores for subcellular localizations and interactions.

Main Methods:

Integrated nine PPI and eight subcellular localization datasets across four species.
Developed a manually curated hierarchical structure of over 1600 subcellular localizations.
Implemented filtering for biologically unlikely interactions based on localization data.
Provided confidence scores for localizations and interactions.

Main Results:

ComPPI offers a comprehensive, compartmentalized view of protein-protein interaction networks.
Users can filter interactions based on shared subcellular localizations.
Predicts compartment-specific biological functions and provides confidence scores.
Supports four species: yeast, C. elegans, D. melanogaster, and H. sapiens.

Conclusions:

ComPPI is a valuable resource for analyzing protein interactions within specific cellular compartments.
Facilitates the study of experimental results in biochemistry and molecular biology.
Aids proteome-wide studies in bioinformatics and network science.
Supports advancements in cellular biology, medicine, and drug design.