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

14.4K
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:
14.4K
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

9.6K
9.6K
Calculating Standard Free Energy Changes02:49

Calculating Standard Free Energy Changes

23.7K
The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
23.7K
Gibbs Free Energy02:39

Gibbs Free Energy

36.2K
One of the challenges of using the second law of thermodynamics to determine if a process is spontaneous is that it requires measurements of the entropy change for the system and the entropy change for the surroundings. An alternative approach involving a new thermodynamic property defined in terms of system properties only was introduced in the late nineteenth century by American mathematician Josiah Willard Gibbs. This new property is called the Gibbs free energy (G) (or simply the free...
36.2K
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

419
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...
419
Conserved Binding Sites01:49

Conserved Binding Sites

4.8K
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...
4.8K

You might also read

Related Articles

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

Sort by
Same author

Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.

Journal of chemical theory and computation·2026
Same author

MOFF2: A Transferable Coarse-Grained Protein Force Field for Predictive Condensate Simulations.

bioRxiv : the preprint server for biology·2026
Same author

From molecular motors to chromosome architecture.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Active regulation of the epidermal growth factor receptor by the membrane bilayer.

eLife·2026
Same author

NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.

Journal of chemical theory and computation·2026
Same author

Chromatin structure and dynamics: Recent advancements.

The Journal of chemical physics·2025
Same journal

Revisiting, Understanding, and Tailoring the Evolution in the Nature of Phase Transitions in Rare-Earth RE<sub>2</sub>In Alloys.

The journal of physical chemistry letters·2026
Same journal

Room-Temperature Quasi-CW Random Lasing in a Tin-Perovskite Ultrathin Film.

The journal of physical chemistry letters·2026
Same journal

Emerging Electride Behavior and Metallization in Molecular Hydrogen under High Pressure.

The journal of physical chemistry letters·2026
Same journal

Surface Electrochemistry of Au(111) in Acetonitrile Based Electrolytes: Formation of a Solvent Related Adsorbed Layer.

The journal of physical chemistry letters·2026
Same journal

Asymmetric Hydration Shell Reveals Interfacial TFSI Organization in Imidazolium Ionic Liquid Films.

The journal of physical chemistry letters·2026
Same journal

Turning 3D Molecular Crystals into 2D Moiré Superlattices with Properties Born Out of Bonding at the Angularly Stacked Interfaces.

The journal of physical chemistry letters·2026
See all related articles

Related Experiment Video

Updated: Nov 12, 2025

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

1.8K

DeepBAR: A Fast and Exact Method for Binding Free Energy Computation.

Xinqiang Ding1, Bin Zhang1

  • 1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.

The Journal of Physical Chemistry Letters
|March 15, 2021
PubMed
Summary
This summary is machine-generated.

We developed DeepBAR, a novel deep generative model method for fast and accurate binding free energy calculations. This efficient approach surpasses traditional methods, offering exact results for drug design applications.

More Related Videos

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions
09:15

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

Published on: November 21, 2017

8.6K
Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy
08:10

Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy

Published on: November 20, 2021

3.2K

Related Experiment Videos

Last Updated: Nov 12, 2025

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

1.8K
Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions
09:15

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

Published on: November 21, 2017

8.6K
Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy
08:10

Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy

Published on: November 20, 2021

3.2K

Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Drug discovery

Background:

  • Calculating binding free energy is crucial for drug design.
  • Current methods face challenges in balancing accuracy and computational efficiency.
  • Existing approaches like MM/GBSA involve approximations for entropic contributions.

Purpose of the Study:

  • Introduce DeepBAR, a new computational method for binding free energy calculation.
  • Enhance the efficiency and accuracy of binding free energy computations.
  • Provide a valuable tool for drug design and discovery.

Main Methods:

  • Utilized deep generative models combined with the Bennett acceptance ratio (BAR) method.
  • Developed the DeepBAR computational approach.
  • Applied DeepBAR to host-guest systems for validation.

Main Results:

  • DeepBAR achieves an order-of-magnitude increase in efficiency compared to the potential of mean force (PMF) method.
  • The method provides exact binding free energy calculations, avoiding approximations.
  • Demonstrated superior performance in host-guest binding free energy calculations.

Conclusions:

  • DeepBAR offers a significant advancement in calculating standard binding free energy.
  • The method provides an accurate and efficient alternative to existing techniques.
  • DeepBAR is poised to become an essential tool in computational drug design.