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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

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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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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...
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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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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.
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Related Experiment Video

Updated: Jul 10, 2025

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
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Introducing the Automated Ligand Searcher.

Luise Jacobsen1, Jonathan Hungerland2, Vladimir Bačić2

  • 1Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.

Journal of Chemical Information and Modeling
|November 20, 2023
PubMed
Summary

The Automated Ligand Searcher (ALISE) software speeds up drug discovery by filtering potential drug molecules. This computational tool successfully identifies promising drug candidates for HIV protease, enhancing development workflows.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Biophysics

Background:

  • Automated computational drug discovery tools are essential for efficient pharmaceutical research.
  • Accurate approximation of ligand-receptor binding free energy is critical for identifying effective drug candidates.
  • Existing workflows can be time-consuming and require significant computational resources.

Purpose of the Study:

  • To introduce the Automated Ligand Searcher (ALISE), a novel computational tool for drug discovery.
  • To present a three-stage workflow within ALISE for approximating ligand-receptor binding free energy.
  • To evaluate the performance and usability of ALISE using a case study.

Main Methods:

  • ALISE employs a three-stage computational workflow: molecular docking, molecular dynamics, and free energy perturbation.
  • The workflow progressively filters out poorly performing ligands.
  • Benchmarking was conducted using known active ligands and decoys for the HIV protease.

Main Results:

  • ALISE successfully filtered out decoys, distinguishing them from known active ligands.
  • The software demonstrated effectiveness in identifying potential drug candidates.
  • The case study validated the computational approach for ligand screening.

Conclusions:

  • ALISE is a comprehensive, automated, and user-friendly software tool.
  • The tool significantly improves and accelerates drug development workflows.
  • ALISE represents a valuable advancement in computational drug discovery.