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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

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...

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Related Experiment Video

Updated: Apr 20, 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 docking: from interaction to interactome.

Ilya A Vakser¹

¹Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas.

Biophysical Journal

|November 25, 2014

Summary

This summary is machine-generated.

Protein-protein docking predicts complex structures, aiding drug design and understanding molecular interactions. Advances focus on modeled structures and high-throughput analysis for large biological networks.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Published on: July 25, 2013

Area of Science:

Computational biophysics
Structural biology
Bioinformatics

Background:

Determining protein-protein complex structures experimentally is challenging.
Computational modeling of protein interactions is crucial due to increasing protein structure data.
Protein-protein docking is vital for fundamental research and drug design.

Purpose of the Study:

To predict the three-dimensional structure of protein-protein complexes.
To provide tools for studying protein interactions and guiding drug discovery.
To address challenges in docking, including conformational changes and low-resolution models.

Main Methods:

Utilizing steric and physicochemical complementarity at the protein interface.
Adapting docking methodologies for lower-resolution and modeled protein structures.
Developing high-throughput approaches for modeling large interaction networks.

Main Results:

Shift towards using lower-resolution modeled structures in docking.
Increased focus on handling conformational flexibility and model inaccuracies.
Community-wide assessments driving improvements in predictive methodologies.

Conclusions:

Protein-protein docking is essential for structural biology and drug design.
Advancements in data resources, computation, and understanding protein interactions facilitate better docking approaches.
Future developments aim for more powerful and accurate docking tools for complex biological systems.