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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 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: Dec 3, 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

Navigating the Global Protein-Protein Interaction Landscape Using iRefWeb.

Andrei L Turinsky¹, Sam Dupont², Alexander Botzki²

¹Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON, Canada. turinsky@sickkids.ca.

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

|October 30, 2020

Summary

This summary is machine-generated.

iRefWeb offers a unified interface to protein-protein interactions from multiple databases. It consolidates and validates data, providing reliable evidence for researchers studying protein networks.

Keywords:

Bioinformatics resources IMEx consortium Interaction networks Literature curation PSI-MI standards Protein–protein interactions Proteomics iRefIndex iRefWeb

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Last Updated: Dec 3, 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

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

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Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Area of Science:

Bioinformatics
Molecular Biology
Computational Biology

Background:

Protein-protein interactions (PPIs) are crucial for cellular functions.
Existing PPI databases often contain redundant and inconsistently annotated data.
A unified and reliable resource for PPI data is needed.

Purpose of the Study:

To present iRefWeb, a web interface for a consolidated collection of protein-protein interactions.
To describe the iRefIndex data-consolidation process for handling redundant and disparate PPI records.
To provide tools for exploring, validating, and comparing PPI data.

Main Methods:

Aggregation of PPI data from major primary databases.
Development of the iRefIndex process to identify redundant protein sequences and integrate disparate data records.
Implementation of a unified web interface (iRefWeb) with data filters and visualization features.

Main Results:

iRefWeb provides access to a large, consolidated collection of protein-protein interactions.
The iRefIndex methodology successfully integrates data despite differences in source database identifiers.
Users can explore PPIs, assess data provenance, and compare curator annotations.

Conclusions:

iRefWeb serves as a valuable, unified resource for exploring protein-protein interactions.
The data consolidation methodology ensures data reliability and consistency.
The portal facilitates a deeper understanding of protein interaction networks.