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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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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:
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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:
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: May 27, 2026

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance
10:07

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

Rationalizing tight ligand binding through cooperative interaction networks.

Bernd Kuhn1, Julian E Fuchs, Michael Reutlinger

  • 1Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland. bernd.kuhn@roche.com

Journal of Chemical Information and Modeling
|November 18, 2011
PubMed
Summary
This summary is machine-generated.

Understanding protein-ligand interactions is key for drug discovery. This study introduces novel computational methods to predict binding hot-spots, improving rational drug design by analyzing noncovalent interactions and their environmental effects.

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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

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Related Experiment Videos

Last Updated: May 27, 2026

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance
10:07

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Ligand modifications can significantly enhance protein binding affinity.
  • Predicting these 'hot-spots' of interaction is crucial for optimizing drug candidates.
  • Current methods often overlook complex interaction dynamics.

Purpose of the Study:

  • To develop new computational approaches for rationalizing and predicting interaction hot-spots in protein-ligand binding.
  • To enhance the understanding of molecular recognition processes.
  • To improve the accuracy of scoring functions for drug design.

Main Methods:

  • A comprehensive set of favorable and unfavorable noncovalent interactions (e.g., halogen bonding, multipolar interactions) were analyzed.
  • A small world network approach was employed to model the environmental modulation of atomic interactions.
  • A new empirical scoring function, ScorpionScore, was derived and validated.

Main Results:

  • The new approach captures local cooperativity effects in binding interactions.
  • ScorpionScore demonstrates improved performance compared to standard methods.
  • Intuitive visualization of interaction networks aids in identifying and rationalizing tight ligand binding.

Conclusions:

  • The study provides a more holistic computational description of protein-ligand binding.
  • The developed methods and scoring function can significantly aid in the rational design of potent therapeutic agents.
  • Visualizing interaction networks is a powerful tool for drug discovery and optimization.