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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...

Protein-Protein Interfaces

Protein-Protein Interfaces

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 Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

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...

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Related Experiment Video

Updated: Oct 29, 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

Databases for Protein-Protein Interactions.

Natsu Nakajima¹, Tatsuya Akutsu², Ryuichiro Nakato³

¹Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan. natsu01zb@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)

|July 8, 2021

Summary

This summary is machine-generated.

This review covers protein-protein interaction databases and computational methods essential for understanding biological processes. It highlights key resources for molecular and systems biology research.

Keywords:

Computational methods Molecular interactions Protein interaction networks Protein structures Protein–protein interactions

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Last Updated: Oct 29, 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

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Area of Science:

Molecular Biology
Systems Biology
Bioinformatics

Background:

Protein-protein interactions (PPIs) are fundamental to cellular functions and biological processes.
Understanding these interactions is crucial for deciphering complex biological systems.
Vast amounts of PPI data have been generated and curated across various species.

Purpose of the Study:

To review prominent databases that store protein-protein interaction information.
To provide an overview of major computational methodologies employed for analyzing PPIs.
To serve as a resource for researchers in molecular and systems biology.

Main Methods:

Literature review of established protein-protein interaction databases.
Survey of widely used computational approaches for PPI analysis.
Synthesis of information on data integration and resource accessibility.

Main Results:

Identification of key databases for PPI data retrieval.
Categorization of prevalent computational methods for PPI network analysis.
Discussion of the significance of these resources in biological research.

Conclusions:

Databases and computational methods are vital tools for studying protein-protein interactions.
Accessible and well-curated resources facilitate advancements in molecular and systems biology.
This review consolidates essential information for researchers in the field.