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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 polypeptide...

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 polypeptide...

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Related Experiment Video

Updated: May 26, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Virtual screening for compounds that mimic protein-protein interface epitopes.

Tim Geppert¹, Felix Reisen, Max Pillong

¹Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Institute of Pharmaceutical Sciences, Wolfgang-Pauli-Str. 10, CH-8093 Zurich, Switzerland.

Journal of Computational Chemistry

|December 14, 2011

Summary

This summary is machine-generated.

This study introduces a computational method to find drugs that block protein-protein interactions (PPIs). The protocol uses predicted interface regions to screen compounds, successfully identifying potential serine protease inhibitors.

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Last Updated: May 26, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

Published on: March 25, 2014

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Area of Science:

Computational drug discovery
Structural bioinformatics
Medicinal chemistry

Background:

Protein-protein interactions (PPIs) are crucial in cellular processes.
Targeting PPIs is a promising strategy for rational drug design.
Developing inhibitors for PPIs presents unique challenges.

Purpose of the Study:

To present a computational protocol for identifying potential protein-protein interaction inhibitors.
To establish a virtual screening framework for drug discovery targeting PPIs.

Main Methods:

Prediction of relevant interface regions (epitopes) on three-dimensional protein models.
Virtual compound screening incorporating two distinct pharmacophore models: autocorrelation vectors and fuzzy labeled graphs.
Proof-of-concept study using a predicted trypsin epitope to identify serine protease inhibitors.

Main Results:

Successful identification of potential serine protease inhibitors.
Demonstration of the utility of the computational screening protocol.
Validation of the proposed framework for identifying PPI inhibitors.

Conclusions:

The developed computational protocol enables rapid identification of PPI inhibitors.
The framework can suggest bioactive tool compounds for further research.
This approach advances rational drug design by targeting PPIs.