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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 polypeptide...

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 polypeptide...

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

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 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 to...

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 to...

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Related Experiment Video

Updated: Jun 27, 2026

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Integrated network analysis platform for protein-protein interactions.

Jianmin Wu¹, Tea Vallenius, Kristian Ovaska

¹Genome-Scale Biology Program, Institute of Biomedicine, University of Helsinki, Haartmaninkatu 8, Helsinki, Finland. jianmin.wu@helsinki.fi

|December 17, 2008

Summary

This summary is machine-generated.

We developed PINA, a web platform for protein-protein interaction (PPI) network analysis. PINA integrates data from six databases, offering tools for network construction, filtering, analysis, and visualization to advance biological discovery.

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Last Updated: Jun 27, 2026

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

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Published on: August 21, 2019

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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

Area of Science:

Bioinformatics
Systems Biology
Computational Biology

Background:

Protein-protein interactions (PPIs) are crucial for cellular functions.
Analyzing large-scale PPI networks is essential for understanding complex biological processes.
Existing tools for PPI network analysis have limitations in data integration and functionality.

Purpose of the Study:

To introduce PINA, a comprehensive web-based platform for protein-protein interaction network analysis.
To integrate data from multiple PPI databases for enhanced analysis.
To provide a user-friendly interface with tools for network construction, filtering, analysis, and visualization.

Main Methods:

Developed a web-based platform (PINA) integrating PPI data from six major databases.
Implemented tools for network construction, data filtering, and advanced network analysis.
Utilized PINA to analyze two human PPI networks.

Main Results:

PINA successfully integrated data from six PPI databases.
Analysis of human PPI networks using PINA revealed potential links between LKB1 and TGFbeta signaling.
The platform identified possible competitive interactors for p53 and c-Jun.

Conclusions:

PINA offers a powerful and integrated solution for PPI network analysis.
The platform facilitates the discovery of novel biological insights, such as signaling pathway associations and protein interaction mechanisms.
PINA enhances the capabilities for researchers studying complex biological networks.