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Related Concept Videos

Protein-protein Interfaces02:04

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 Interfaces02:04

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...
Conserved Binding Sites01:49

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 analyses the...
Conserved Binding Sites01:49

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 analyses the...
Ligand Binding Sites02:40

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...
Ligand Binding Sites02:40

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: Jun 27, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Predicting druggable binding sites at the protein-protein interface.

Jonathan C Fuller1, Nicholas J Burgoyne, Richard M Jackson

  • 1Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

Drug Discovery Today
|December 2, 2008
PubMed
Summary

Protein-protein interactions (PPIs) are promising drug targets. New algorithms reveal differences in binding pockets, suggesting strategies to target multiple small pockets for successful drug discovery.

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Last Updated: Jun 27, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

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:

  • Medicinal Chemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Protein-protein interactions (PPIs) are implicated in numerous disease pathways, presenting significant therapeutic opportunities.
  • Historically, PPIs were considered 'undruggable,' but recent advancements are challenging this notion.
  • Effective drug discovery targeting PPIs requires understanding their unique binding site characteristics.

Purpose of the Study:

  • To investigate the distinct structural features of binding pockets involved in protein-protein interactions (PPIs).
  • To compare these PPI-specific pockets with those of protein-ligand interactions (PLIs) targeted by existing drugs.
  • To inform novel drug discovery strategies for targeting PPIs.

Main Methods:

  • Development and application of novel pocket-finding algorithms.
  • Comparative analysis of binding pocket geometries in PPIs versus PLIs.
  • Identification of key structural differences between PPI and PLI binding sites.

Main Results:

  • Pocket-finding algorithms revealed significant differences between PPI and PLI binding pockets.
  • PPIs are characterized by distinct pocket architectures compared to traditional drug targets.
  • Current drug discovery approaches may not be optimal for PPI targets.

Conclusions:

  • PPIs represent a viable and increasingly druggable target class.
  • Targeting multiple small pockets within the PPI interface simultaneously is a promising therapeutic strategy.
  • Further development of specialized algorithms and approaches is crucial for advancing PPI-targeted drug discovery.