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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-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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:
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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 10, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
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Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Computational methodologies for compound database searching that utilize experimental protein-ligand interaction

Lu Tan1, Jose Batista, Jürgen Bajorath

  • 1Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany.

Chemical Biology & Drug Design
|July 20, 2010
PubMed
Summary
This summary is machine-generated.

This study reviews methods combining ligand- and structure-based approaches for computational screening. It highlights interaction-based techniques and the novel interacting fragment method for enhanced drug discovery.

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Protein Target Prediction and Validation of Small Molecule Compound
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Protein Target Prediction and Validation of Small Molecule Compound

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Last Updated: Jun 10, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
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Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Protein Target Prediction and Validation of Small Molecule Compound
10:21

Protein Target Prediction and Validation of Small Molecule Compound

Published on: February 23, 2024

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Bioinformatics

Background:

  • Ligand-based and target structure-based methods are key in virtual screening.
  • Current methodologies lack full integration of these distinct approaches.
  • Protein-ligand interaction information is crucial for effective screening and filtering.

Purpose of the Study:

  • To provide an overview of integrated ligand- and structure-based computational screening methods.
  • To review approaches utilizing protein-ligand interaction data.
  • To discuss novel methods bridging the gap between ligand- and structure-based techniques.

Main Methods:

  • Review of existing attempts to combine ligand- and structure-based screening.
  • Analysis of interaction-based approaches (pharmacophore modeling, fingerprint encoding).
  • Discussion of the interacting fragment approach for 3D-to-2D similarity searching.

Main Results:

  • Interaction-based methods are versatile for virtual screening tasks.
  • These methods aid in postprocessing docking poses, prioritizing binding modes, selectivity analysis, and similarity searching.
  • The interacting fragment approach effectively integrates 3D interaction data into 2D similarity searches.

Conclusions:

  • Integrating ligand- and structure-based methods offers a more comprehensive virtual screening strategy.
  • Interaction-based approaches significantly enhance the efficiency and accuracy of drug discovery pipelines.
  • The interacting fragment method represents a promising advancement in bridging computational screening methodologies.