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

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 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:
Chemical and Solubility Equilibria02:21

Chemical and Solubility Equilibria

The free energy change associated with dissolving a solute in a liter of solvent is called the free energy of a solution, ΔGsolution. The overall ΔGsolution is expressed as the balance of ΔGinteraction against the always-favorable free-energy of mixing, ΔGmixing. Solution formation is favorable if  ΔGsolution is less than zero, whereas it is unfavorable if ΔGsolution is greater than zero. In short, for a solution to form and complete dissolution to take place, the Gibbs energy change must be...
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...
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...
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...

You might also read

Related Articles

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

Sort by
Same author

Multifunctional ACE2-nanobody fusion design for pan-specific neutralization and cardiovascular protection in SARS coronavirus infection.

Antimicrobial agents and chemotherapy·2026
Same author

CHO Cell Line Selection through Multi-Criteria Analysis Reveals Critical Impact of Gas Overlay.

Biotechnology journal·2026
Same author

Global Protein Interaction Network for <i>Trypanosoma cruzi</i>.

Journal of proteome research·2025
Same author

Engineered multifunctional transforming growth factor-β type II receptor ectodomain fusions for oncology applications.

Frontiers in oncology·2025
Same author

Optimization of synthetic human V<sub>H</sub> affinity and solubility through in vitro affinity maturation and minimal camelization.

Protein science : a publication of the Protein Society·2025
Same author

AI-augmented physics-based docking for antibody-antigen complex prediction.

Bioinformatics (Oxford, England)·2025
Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

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

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

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

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

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

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

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

3D Chromatin Architecture During Early Development: New Methods and New Findings.

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

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

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

Related Experiment Video

Updated: May 26, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

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

Published on: May 9, 2025

The solvated interaction energy method for scoring binding affinities.

Traian Sulea1, Enrico O Purisima

  • 1Biotechnology Research Institute, National Research Council, Ottawa, ON, Canada.

Methods in Molecular Biology (Clifton, N.J.)
|December 21, 2011
PubMed
Summary
This summary is machine-generated.

Solvated interaction energy (SIE) accurately predicts ligand-binding affinities by combining force-field energy with desolvation costs. This physics-based scoring function was applied to molecular dynamics simulations for binding free energy estimation.

More Related Videos

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

Related Experiment Videos

Last Updated: May 26, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

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

Published on: May 9, 2025

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

Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Biophysics

Background:

  • Ligand-binding affinity prediction is crucial for drug discovery.
  • Existing scoring functions often neglect desolvation effects.
  • Solvated interaction energy (SIE) offers a physics-based approach.

Purpose of the Study:

  • To apply the calibrated solvated interaction energy (SIE) scoring function.
  • To estimate binding free energies using molecular dynamics (MD) trajectories.
  • To validate SIE's performance in predicting protein-ligand binding.

Main Methods:

  • Utilized a physics-based scoring function, solvated interaction energy (SIE).
  • Incorporated force-field interaction energy and desolvation cost.
  • Employed molecular dynamics (MD) simulations of protein-ligand complexes.
  • Applied previously calibrated parameters for SIE.

Main Results:

  • Demonstrated the application of SIE for binding free energy estimation.
  • Successfully integrated desolvation costs into the scoring function.
  • Showcased the utility of SIE with MD trajectories.

Conclusions:

  • Solvated interaction energy (SIE) is a viable method for predicting binding free energies.
  • The approach effectively models the energetic contributions of solvation.
  • SIE enhances the accuracy of ligand-binding affinity predictions.