Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

The Equilibrium Binding Constant and Binding Strength

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:

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

Ligand Binding Sites

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...

Conserved Binding Sites

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...

You might also read

Related Articles

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

Sort by

Same author

Near-Infrared Polarity-Sensitive Fluorescent Probe for Distinguishing Normal and Cancer Cells and Imaging Mitochondrial Polarity Changes during Drug-Induced Liver Injury.

Analytical chemistry·2026

Same author

Integrative PANoptosis-focused omics analysis uncovers GSDMC as a candidate biomarker in breast cancer.

Frontiers in cell and developmental biology·2026

Same author

Role of Various Commercial <i>Saccharomyces cerevisiae</i> in Secondary Fermentation of Pineapple Glutinous Rice Wine: Insights into Volatile Profiling by GC-IMS and Sensory Attributes.

Foods (Basel, Switzerland)·2026

Same author

Histone acetyltransferase Kat2a regulates glioma stem cell differentiation via Hsp90aa1-dependent oxidative phosphorylation.

Biochemical pharmacology·2026

Same author

An engineered aryl sulfotransferase for the biosynthesis of glycosaminoglycans.

International journal of biological macromolecules·2026

Same author

Macrophage morphology in the tumor microenvironment predicts metachronous liver metastasis in gastric cancer: establishment and validation of a predictive model.

Frontiers in immunology·2026

Search research articles

Related Experiment Video

Updated: Feb 16, 2026

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Published on: November 21, 2017

Trypsin-Ligand binding affinities calculated using an effective interaction entropy method under polarized force

Yalong Cong¹, Mengxin Li¹, Guoqiang Feng¹

¹Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.

Scientific Reports

|December 20, 2017

Summary

A new polarized protein-specific charge (PPC) force field and interaction entropy (IE) method improve molecular dynamics (MD) simulations for trypsin-ligand binding, yielding more accurate binding free energy calculations than traditional methods.

More Related Videos

Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions

Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions

Published on: October 21, 2016

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

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

Published on: June 20, 2025

Related Experiment Videos

Last Updated: Feb 16, 2026

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Published on: November 21, 2017

Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions

Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions

Published on: October 21, 2016

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

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

Published on: June 20, 2025

Area of Science:

Computational chemistry
Molecular modeling
Biophysics

Background:

Molecular dynamics (MD) simulations are crucial for understanding molecular interactions.
Accurate force fields and entropy calculation methods are essential for reliable simulation results.
Traditional methods like AMBER force field and normal mode (Nmode) analysis have limitations in predicting binding free energies.

Purpose of the Study:

To investigate the interaction mechanism of trypsin-ligand binding using MD simulations.
To compare the performance of the AMBER and polarized protein-specific charge (PPC) force fields.
To evaluate a new highly efficient interaction entropy (IE) method for entropy change calculations.

Main Methods:

Molecular dynamics (MD) simulations in explicit water.
Utilized AMBER and polarized protein-specific charge (PPC) force fields.
Employed the interaction entropy (IE) method and compared it with the normal mode (Nmode) method for entropy change calculation.

Main Results:

The PPC force field demonstrated greater stability in terms of root-mean-square deviation (RMSD), B-factor, and hydrogen bonds compared to the AMBER force field.
The IE method proved superior to the Nmode method for entropy change calculations.
The PPC force field combined with the IE method yielded binding free energy values closer to experimental data.

Conclusions:

The polarized protein-specific charge (PPC) force field and the interaction entropy (IE) method are critical for accurate molecular dynamics (MD) simulations and free energy calculations.
The PPC force field better preserves critical hydrogen bonds in trypsin-ligand interactions.
The developed IE method offers a more accurate approach to entropy change calculation in molecular simulations.