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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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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.
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...
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Ligand Binding Sites02:40

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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.
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Ligand Binding and Linkage00:49

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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 and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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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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Updated: Dec 27, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware
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Investigating Cryptic Binding Sites by Molecular Dynamics Simulations.

Antonija Kuzmanic1, Gregory R Bowman2, Jordi Juarez-Jimenez3

  • 1Department of Chemistry and Institute of Structural and Molecular Biology, University College London, London WC1E 0AJ, United Kingdom.

Accounts of Chemical Research
|March 6, 2020
PubMed
Summary
This summary is machine-generated.

Molecular simulations can identify cryptic binding sites, which are hidden protein pockets crucial for drug discovery. Advanced computational methods help uncover these sites on difficult-to-target proteins.

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Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Cryptic binding sites are transient protein pockets, often undetectable by standard experimental methods.
  • These sites offer potential for targeting challenging proteins previously considered undruggable.
  • Identifying cryptic sites is difficult due to their dynamic and hidden nature.

Purpose of the Study:

  • To review advances in using molecular simulations for cryptic binding site identification.
  • To discuss challenges and solutions in computational approaches for cryptic site discovery.
  • To highlight the role of cryptic sites in targeting difficult proteins for drug development.

Main Methods:

  • Atomistic molecular simulations
  • Mixed-solvent simulations
  • Metadynamics
  • Markov state models
  • Enhanced sampling techniques

Main Results:

  • Molecular simulations effectively identify and characterize cryptic binding sites.
  • Enhanced sampling methods provide insights into site opening mechanisms and ligand binding.
  • Predicted cryptic sites have been used to design novel ligands for drug discovery.
  • Free energy landscapes and kinetics of site opening and ligand binding can be computed.

Conclusions:

  • Molecular simulations are essential for discovering and characterizing cryptic binding sites.
  • Advanced computational methods offer powerful tools for drug discovery, especially for challenging targets.
  • Further development of simulation techniques is needed to overcome current challenges in the field.