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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 Organization

Protein Organization

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Related Experiment Video

Updated: Apr 15, 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

Protein-protein interaction databases.

Damian Szklarczyk¹, Lars Juhl Jensen

¹Faculty of Health Sciences, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, København N, Denmark.

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

|April 11, 2015

Summary

This summary is machine-generated.

Protein-protein interaction databases, built from literature and computational predictions, are crucial for research. Scientists must understand their limitations regarding accuracy and comprehensiveness for reliable analysis.

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Last Updated: Apr 15, 2026

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

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Published on: March 3, 2015

Identifying Protein-protein Interaction Sites Using Peptide Arrays

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Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

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Published on: July 6, 2014

Area of Science:

Biochemistry
Bioinformatics
Computational Biology

Background:

Extensive curation of scientific literature and computational predictions have generated large protein-protein interaction (PPI) databases.
These repositories are fundamental for analyzing experiments and guiding new research directions in molecular biology.

Purpose of the Study:

To provide an overview of widely used PPI databases.
To describe the methods used for data acquisition, integration, and prediction of interactions.
To highlight the inherent trade-offs between database comprehensiveness and accuracy.

Main Methods:

Review of existing protein-protein interaction databases.
Analysis of data gathering, combination, and prediction methodologies.
Evaluation of database accuracy and comprehensiveness.

Main Results:

Identification of key PPI databases and their underlying methods.
Discussion of the balance between data breadth and reliability.
Pinpointing critical considerations for researchers using PPI data.

Conclusions:

Protein-protein interaction databases are invaluable tools but require careful usage.
Scientists must be aware of potential pitfalls, particularly the accuracy-comprehensiveness trade-off, before employing these databases in analyses.