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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...
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...
Protein Networks02:26

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-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...

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Updated: May 13, 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 where small molecules bind at protein-protein interfaces.

Peter Walter1, Jennifer Metzger, Christoph Thiel

  • 1Center for Bioinformatics, Saarland University, Saarbrücken, Germany.

Plos One
|March 19, 2013
PubMed
Summary
This summary is machine-generated.

Researchers identified conserved residues at protein-protein interfaces that bind small molecules, aiding drug design. A new classifier predicts these drug-target sites on protein interfaces.

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

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Related Experiment Videos

Last Updated: May 13, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Published on: January 26, 2024

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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:

  • Biochemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Small molecules can modulate protein-protein interactions (PPIs) by binding to interfaces.
  • Identifying PPI interfaces amenable to small molecule binding is crucial for drug design.

Purpose of the Study:

  • To identify characteristics of protein interface residues that bind small molecules.
  • To develop a predictive model for identifying small molecule binding sites at PPI interfaces.

Main Methods:

  • Collected 175 protein-protein (PP) and protein-ligand (PL) complex structures.
  • Analyzed sequence conservation, pocket propensity, and solvent accessibility of interface residues.
  • Developed a statistical classifier to predict small molecule binding patches.

Main Results:

  • Interface residues binding both proteins and small molecules are more conserved and pocket-like.
  • The developed classifier successfully predicted small molecule binding patches on over 10,000 interfaces.
  • Predicted binding patches were validated in complexes related to apoptosis.

Conclusions:

  • Conserved, pocket-like residues at PPI interfaces are key targets for small molecule binders.
  • The predictive classifier can guide the design of novel therapeutics targeting PPIs.
  • This approach enhances the potential of PPIs as drug targets.