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

The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

14.2K
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:
14.2K
Ligand Binding Sites02:40

Ligand Binding Sites

14.1K
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...
14.1K
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

346
Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
346
Conserved Binding Sites01:49

Conserved Binding Sites

4.6K
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...
4.6K

You might also read

Related Articles

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

Sort by
Same author

Tetrapeptide inhibitors of BACE-1 revealed by combined data-driven screening and physics-based free-energy refinement.

Molecular diversity·2026
Same author

Computational Drug Repurposing Predicts FDA-Approved Drugs as Potential Inhibitors of Chikungunya Virus nsP2 Protease.

The journal of physical chemistry. B·2026
Same author

Structure-Based Drug Design Targeting Topoisomerase II Alpha: Discovery of Potential Antitumor Xanthone Derivatives.

Molecules (Basel, Switzerland)·2026
Same author

Dynamics of Aβ42 Tetramer by REST2-CHARMM36m Simulations.

The journal of physical chemistry. B·2026
Same author

Identifying Potential BACE1 Inhibitors from the ChEMBL Database Using Machine Learning and Atomistic Simulation Approaches.

ACS omega·2026
Same author

Nitric oxide and α-glucosidase inhibitors from Ludwigia adscendens: An integrated in vitro and in silico study.

Bioorganic & medicinal chemistry letters·2026
Same journal

Tracking Synthetic Adhesins on Bacterial Surfaces with Immunofluorescence Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Post-Selection Methods for Analyzing mRNA Display Selections and Optimization of Hits.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Engineering and Adapting Disulfide-Containing Proteins to Enable Intracellular Functionality.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

AI-Driven Protein Research: From Prediction to Design.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for the In Vitro Selection of Protein and Peptide Libraries Using mRNA Display.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Oct 10, 2025

An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions
08:40

An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions

Published on: March 14, 2016

19.4K

Umbrella Sampling-Based Method to Compute Ligand-Binding Affinity.

Son Tung Ngo1,2, Minh Quan Pham3,4

  • 1Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam. ngosontung@tdtu.edu.vn.

Methods in Molecular Biology (Clifton, N.J.)
|December 10, 2021
PubMed
Summary
This summary is machine-generated.

This study demonstrates how umbrella sampling simulations can effectively determine protein-inhibitor binding affinity. This method models the binding pathway, offering insights into drug discovery and protein-ligand interactions.

Keywords:
Biased samplingLigand-binding free energyPotential of mean forceSteered MDUmbrella samplingWHAM calculation

More Related Videos

Isothermal Titration Calorimetry for Measuring Macromolecule-Ligand Affinity
08:45

Isothermal Titration Calorimetry for Measuring Macromolecule-Ligand Affinity

Published on: September 7, 2011

53.3K
Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry
13:26

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Published on: September 13, 2014

62.1K

Related Experiment Videos

Last Updated: Oct 10, 2025

An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions
08:40

An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions

Published on: March 14, 2016

19.4K
Isothermal Titration Calorimetry for Measuring Macromolecule-Ligand Affinity
08:45

Isothermal Titration Calorimetry for Measuring Macromolecule-Ligand Affinity

Published on: September 7, 2011

53.3K
Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry
13:26

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Published on: September 13, 2014

62.1K

Area of Science:

  • Biochemistry
  • Computational Biology
  • Pharmacology

Background:

  • Proteins often feature solvent-exposed binding clefts, facilitating inhibitor interaction without major conformational changes.
  • Understanding protein-inhibitor dynamics is crucial for drug development.

Purpose of the Study:

  • To outline a computational method for calculating protein-inhibitor binding affinity.
  • To demonstrate the utility of umbrella sampling for analyzing binding pathways.

Main Methods:

  • Utilized umbrella sampling (US) simulations to model protein-inhibitor binding/unbinding pathways.
  • Applied harmonic restraints to Cα atoms of proteins during simulations.
  • Employed the weighted histogram analysis method (WHAM) to estimate the potential of mean force (PMF).

Main Results:

  • Successfully estimated the PMF along the binding pathway.
  • Calculated binding affinity by analyzing the PMF difference between bound and unbound states.

Conclusions:

  • Umbrella sampling provides a viable method for computing binding affinities of protein-inhibitor complexes.
  • This approach simplifies the analysis of straightforward binding/unbinding pathways.