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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 21, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Information-driven structural modelling of protein-protein interactions.

João P G L M Rodrigues¹, Ezgi Karaca, Alexandre M J J Bonvin

¹Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.

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

|October 22, 2014

Summary

Protein-protein docking predicts complex structures using physics and experimental data. The HADDOCK software is a leading information-driven approach for modeling protein complexes, including multi-body systems.

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Area of Science:

Computational biology
Structural biology
Biophysics

Background:

Protein-protein interactions are fundamental to cellular processes.
Predicting the structure of protein complexes is crucial for understanding their function.
Existing docking methods often require integration of experimental or bioinformatics data for accuracy.

Purpose of the Study:

To summarize experimental information used to guide protein-protein docking predictions.
To detail the HADDOCK docking protocol for predicting protein complex structures.
To illustrate recent advancements in modeling multi-body systems and large conformational changes.

Main Methods:

Utilizing physics-based principles combined with information-driven strategies.
Employing the HADDOCK (High Ambiguity Driven protein-DOCKing) software.
Presenting a tutorial example for classical protein-protein docking.
Discussing methods for modeling multi-protein complexes and significant conformational shifts.

Main Results:

HADDOCK is a highly successful information-driven protein-protein docking approach.
Experimental and bioinformatics data significantly enhance docking prediction accuracy.
The HADDOCK protocol effectively models classical protein-protein docking scenarios.
Recent developments extend HADDOCK's capabilities to complex systems.

Conclusions:

Information-driven approaches, exemplified by HADDOCK, are state-of-the-art for protein-protein docking.
The HADDOCK protocol provides a robust framework for predicting protein complex structures.
HADDOCK's adaptability allows for modeling of complex biological systems and conformational dynamics.