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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 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 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...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

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Related Experiment Video

Updated: Jun 22, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

PPInterface: A Comprehensive Dataset of 3D Protein-Protein Interface Structures.

Zeynep Abali¹, Zeynep Aydin¹, Moaaz Khokhar²

¹Computational Science and Engineering Graduate Program, Koc University, Istanbul 34450, Turkey.

Journal of Molecular Biology

|June 27, 2024

Summary

This summary is machine-generated.

The PPInterface dataset offers extensive structural data on protein-protein interactions, extracted from the Protein Data Bank. This resource aids researchers in exploring protein complex structures and interactions.

Keywords:

3D Protein-protein interface dataset Dataset Interface visualization Protein interfaces Protein–protein complexes Protein–protein interactions

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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Structural Biology
Bioinformatics
Computational Biology

Background:

Protein-protein interactions (PPIs) are crucial for cellular functions.
Understanding the structural basis of PPIs is essential for biological research.
Existing structural databases may not offer comprehensive coverage of protein interfaces.

Purpose of the Study:

To create the most comprehensive dataset of protein-protein interface structures.
To develop an accessible web server for querying and visualizing interface data.
To facilitate research on the structural properties of protein-protein interactions.

Main Methods:

Extraction of interface structures from over 215,000 three-dimensional protein structures in the Protein Data Bank (PDB).
Compilation of 815,082 unique protein-protein interface structures.
Development of a user-friendly web server for data access and visualization.

Main Results:

The PPInterface dataset is the largest collection of protein-protein interface structures to date.
The dataset includes a diverse range of protein complexes.
The web server provides efficient search, download, and visualization capabilities.

Conclusions:

The PPInterface dataset and web server significantly enhance the accessibility and utility of structural information on protein-protein interactions.
This resource will accelerate research in structural biology and drug discovery.
It provides a valuable platform for exploring the structural diversity of protein complexes.