Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

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...
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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Differences in reactive metabolite formation and cytochrome P450 binding between acetaminophen and its bicyclo[1.1.1]pentane bioisostere.

Drug metabolism and pharmacokinetics·2026
Same author

Effect of Cytochrome P450 3A4 Genetic Polymorphisms on Heme Recognition by Using Molecular Dynamics Simulations.

Biological & pharmaceutical bulletin·2026
Same author

Comprehensive functional characterization of rare and known CYP2E1 allelic variants identified in a Japanese population.

Biochemical pharmacology·2025
Same author

Investigation of the Effect of C-Terminal Adjacent Phenylalanine Residues on Asparagine Deamidation by Quantum Chemical Calculations.

International journal of molecular sciences·2025
Same author

Molecular Dynamics Simulations of Monomeric and Tetrameric Amyloid β<sub>1-42</sub> Peptides with d-Aspartic Acid Residues.

Chembiochem : a European journal of chemical biology·2025
Same author

Quantum Chemical Calculations of the Nonenzymatic Bicarbonate Ion-Catalyzed Lactamization of Ornithine Residues to Identify the Components of Primitive Proteins.

The journal of physical chemistry. A·2025

Related Experiment Video

Updated: May 28, 2026

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

[Development and validation of programs for ligand-binding-pocket search].

Akifumi Oda1

  • 1Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, Sendai, Japan. oda@tohoku-pharm.ac.jp

Yakugaku Zasshi : Journal of the Pharmaceutical Society of Japan
|October 4, 2011
PubMed
Summary

This study introduces HBOP, a new program for identifying protein ligand-binding pockets using hydrophobicity. HBOP demonstrates that physicochemical properties improve pocket detection efficiency in structure-based drug design.

More Related Videos

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

Related Experiment Videos

Last Updated: May 28, 2026

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

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:

  • Biochemistry
  • Computational Biology
  • Drug Discovery

Context:

  • Structure-based drug design (SBDD) relies on identifying protein ligand-binding pockets.
  • Current computational methods for pocket detection use either geometric properties or a combination of geometry and physicochemical properties.

Purpose:

  • To develop and evaluate HBOP (Hydrophobicity On a Protein), a novel program for ligand-binding pocket detection.
  • To assess the efficacy of using hydrophobic potentials in identifying protein-ligand interaction sites.

Summary:

  • HBOP utilizes hydrophobic potentials derived from experimental functions to locate ligand-binding pockets, recognizing the critical role of hydrophobicity in protein-ligand binding.
  • The program was evaluated against existing methods, comparing approaches based solely on geometric properties versus those incorporating physicochemical information.

Impact:

  • The evaluation results indicate that computational methods incorporating physicochemical properties, such as HBOP, are more efficient at discovering actual ligand-binding pockets compared to geometry-only methods.
  • This finding can enhance the accuracy and efficiency of drug design by improving the identification of potential drug targets and binding sites.