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Related Concept Videos

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...
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...
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 and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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Related Experiment Video

Updated: Jun 24, 2026

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

Binding site detection and druggability index from first principles.

Jesus Seco1, F Javier Luque, Xavier Barril

  • 1Institucio Catalana de Recerca i Estudis Avancats (ICREA), Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.

Journal of Medicinal Chemistry
|March 20, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a novel molecular dynamics method to identify potential drug binding sites on proteins. The approach accurately predicts druggable pockets and binding affinities, offering a new tool for drug discovery.

Related Experiment Videos

Last Updated: Jun 24, 2026

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:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Identifying specific binding sites on protein surfaces is crucial for developing effective drugs.
  • Organic solvents have been observed to bind to these critical locations in X-ray crystallography and NMR experiments.

Purpose of the Study:

  • To develop and validate a computational method for identifying druggable protein binding sites.
  • To assess the potential of small organic molecules to bind to these sites and predict maximal drug affinity.

Main Methods:

  • Utilizing molecular dynamics simulations with a binary solvent to mimic experimental observations.
  • Analyzing simulation data to calculate protein-small molecule interaction free energies.

Main Results:

  • The molecular dynamics approach successfully reproduced the binding of organic solvents to protein sites.
  • Accurate predictions of druggable sites, protein-protein interaction sites, and low-affinity binding sites were achieved for pharmacologically relevant proteins.

Conclusions:

  • This method provides the first druggability index independent of surface descriptors.
  • The approach is suitable for studying unconventional targets like protein-protein interactions and allosteric sites, advancing drug discovery strategies.