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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...
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:
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: May 19, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

A genetic algorithm-based protocol for docking ensembles of small ligands using experimental restraints.

R P Meadows1, P J Hajduk

  • 1Pharmaceutical Products Division, Abbott Laboratories, 60064, Abbott Park, IL, USA.

Journal of Biomolecular NMR
|August 23, 2012
PubMed
Summary
This summary is machine-generated.

A genetic algorithm effectively docks flexible ligands to proteins using NMR data. This method identifies the minimum ligand orientations needed for experimental restraints, providing structural insights.

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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

Published on: October 26, 2015

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Last Updated: May 19, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 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 Biology
  • Biophysics
  • Molecular Modeling

Background:

  • Protein-ligand interactions are crucial in biological processes.
  • Nuclear Magnetic Resonance (NMR) spectroscopy provides distance restraints for molecular modeling.
  • Docking flexible ligands to protein targets remains computationally challenging.

Purpose of the Study:

  • To develop and validate a genetic algorithm (GA) for docking flexible ligands to protein receptors.
  • To utilize NMR-derived distance restraints within the GA framework.
  • To determine the minimum number of ligand conformations required to satisfy experimental constraints.

Main Methods:

  • Representing ligand translations, rotations, and dihedral angles as binary strings for GA evolution.
  • Employing genetic operators: cross-over, mutation, migration, and selection.
  • Defining a fitness function incorporating distance, dihedral, and van der Waals restraints.

Main Results:

  • The GA successfully docked ligands to a model system and the streptavidin-biotin complex.
  • Low-energy conformations were achieved using simulated intermolecular distance restraints.
  • The method accurately identified ligand positions in two distinct binding sites simultaneously.
  • No energetic benefit was observed with additional ligand conformations beyond those satisfying restraints.

Conclusions:

  • The GA-based method is effective for docking flexible ligands using NMR constraints.
  • The approach efficiently determines the minimal ligand orientations for experimental data.
  • This method provides valuable structural information for multiple binding sites.