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

Conserved Binding Sites01:49

Conserved Binding Sites

4.1K
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...
4.1K
Ligand Binding Sites02:40

Ligand Binding Sites

11.8K
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...
11.8K
Ligand Binding Sites02:40

Ligand Binding Sites

6.0K
6.0K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.5K
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...
12.5K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.4K
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...
4.4K
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

10.6K
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:
10.6K

You might also read

Related Articles

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

Sort by
Same author

Self-referential processing as the biological switch between classical and quantum functioning of the brain.

Frontiers in human neuroscience·2026
Same author

Editorial: Alleviating age-related disease burden.

Frontiers in aging·2026
Same author

Molecular Simulations of Biomembranes: From Biophysics Fundamentals to Biological Function.

Membranes·2026
Same author

Non-linearity, complexity, and quantization concepts in biology.

Frontiers in human neuroscience·2026
Same author

Exploring potential size-dependent effects of Fibonacci-based acoustic binary strings on cells as measured by cell death and cell aggregation patterns.

Bio Systems·2026
Same author

Basic Science and Pathogenesis.

Alzheimer's & dementia : the journal of the Alzheimer's Association·2025
Same journal

Characterization of putative proteins encoded by variable ORFs in white spot syndrome virus genome.

BMC structural biology·2019
Same journal

Correction to: Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region.

BMC structural biology·2019
Same journal

Effect of low complexity regions within the PvMSP3α block II on the tertiary structure of the protein and implications to immune escape mechanisms.

BMC structural biology·2019
Same journal

QRNAS: software tool for refinement of nucleic acid structures.

BMC structural biology·2019
Same journal

Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region.

BMC structural biology·2019
Same journal

A new technique for predicting intrinsically disordered regions based on average distance map constructed with inter-residue average distance statistics.

BMC structural biology·2019
See all related articles

Related Experiment Video

Updated: Apr 26, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.8K

A simple method for finding a protein's ligand-binding pockets.

Seyed Majid Saberi Fathi, Jack A Tuszynski1

  • 1Department of Physics, University of Alberta, Edmonton, Alberta, Canada. jackt@ualberta.ca.

BMC Structural Biology
|July 21, 2014
PubMed
Summary
This summary is machine-generated.

This study introduces a rapid computational method using geometric and biochemical properties to identify protein ligand-binding pockets. This approach aids in protein classification and accelerates drug discovery.

More Related Videos

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

287
Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

3.2K

Related Experiment Videos

Last Updated: Apr 26, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.8K
A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

287
Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

3.2K

Area of Science:

  • Computational biology
  • Structural bioinformatics

Background:

  • A novel protein-clustering strategy is presented.
  • The method utilizes computational geometry to predict and characterize ligand-binding pockets in protein structures.
  • Biochemical properties are integrated with geometrical features to identify active site pockets.

Purpose of the Study:

  • To develop a simple, rapid, and cost-effective computational method for protein analysis.
  • To predict and characterize ligand-binding pockets for protein classification.
  • To aid in reducing the time and cost associated with drug discovery.

Main Methods:

  • Application of computational geometry techniques.
  • Analysis of protein structure geometry.
  • Incorporation of biochemical properties for pocket recognition.

Main Results:

  • The developed method demonstrates good agreement with established empirical results.
  • Successful prediction and characterization of ligand-binding pockets.

Conclusions:

  • The presented method offers a low-cost, rapid computational approach for classifying proteins and biomolecules.
  • This strategy has the potential to significantly reduce the cost and time required for drug discovery efforts.