Jove
Visualize
Contact Us

Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

14.9K
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...
14.9K
Ligand Binding Sites02:40

Ligand Binding Sites

8.7K
8.7K
Comparing the Survival Analysis of Two or More Groups01:20

Comparing the Survival Analysis of Two or More Groups

573
Survival analysis is a cornerstone of medical research, used to evaluate the time until an event of interest occurs, such as death, disease recurrence, or recovery. Unlike standard statistical methods, survival analysis is particularly adept at handling censored data—instances where the event has not occurred for some participants by the end of the study or remains unobserved. To address these unique challenges, specialized techniques like the Kaplan-Meier estimator, log-rank test, and...
573
Metal-Ligand Bonds02:51

Metal-Ligand Bonds

24.0K
The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
24.0K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

5.5K
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...
5.5K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.0K
4.0K

You might also read

Related Articles

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

Sort by
Same author

Quantum algorithms for ligand design in drug discovery.

Expert opinion on drug discovery·2026
Same author

Molecular design drives nanoarchitecture in self-assembling antimicrobial peptides.

Trends in biochemical sciences·2025
Same author

Exploring Daptomycin Hypersensitivity in <i>Enterococcus faecium</i>: The Impact of LafB Mutation on Bacterial Virulence.

International journal of molecular sciences·2025
Same author

Structure and dynamics of the staphylococcal pyridoxal 5-phosphate synthase complex reveal transient interactions at the enzyme interface.

The Journal of biological chemistry·2024
Same author

The CDR3 region as the major driver of TREM-1 interaction with its ligands, an <i>in silico</i> characterization.

Computational and structural biotechnology journal·2023
Same author

Immunoinformatics-guided design of a multi-valent vaccine against Rotavirus and Norovirus (ChRNV22).

Computers in biology and medicine·2023
Same journal

Editorial: Epigenetic and genetic mechanisms underlying cardiovascular diseases and neurodevelopmental disorders, volume II.

Frontiers in molecular biosciences·2026
Same journal

Integrated transcriptomic profiling reveals oncogenic pathways and chimeric transcripts in equine sarcoid lesions with predominant BPV1 detection.

Frontiers in molecular biosciences·2026
Same journal

Mesenchymal stem cells-derived extracellular vesicles as a novel drug delivery carrier: engineering strategies and clinical safety estimation.

Frontiers in molecular biosciences·2026
Same journal

Preparation and analysis of tobacco glycosides, and the relationship between glycoside aglycones and pyrolysis products: a review.

Frontiers in molecular biosciences·2026
Same journal

Peritoneal metastasis in pancreatic cancer: molecular mechanisms, microenvironmental remodeling, and emerging intraperitoneal interventions.

Frontiers in molecular biosciences·2026
Same journal

Insights from LC-MS-based cerebrospinal fluid metabolomics in tuberculous meningitis.

Frontiers in molecular biosciences·2026
See all related articles
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 Experiment Video

Updated: Jan 21, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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

Published on: June 20, 2025

1.2K

Comparative Analysis of Electrostatic Models for Ligand Docking.

Geraldo Rodrigues Sartori1, Alessandro S Nascimento1

  • 1São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil.

Frontiers in Molecular Biosciences
|July 24, 2019
PubMed
Summary
This summary is machine-generated.

Comparing electrostatic models for molecular docking, the Poisson-Boltzmann (PB) model improved ligand pose and identification accuracy over the classical Coulomb model. PB models offer a better balance for molecular interactions and scoring.

Keywords:
CoulombPoisson-Boltzmannelectrostatic energyligand dockingpolar interactions

More Related Videos

Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16
06:03

Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16

Published on: July 15, 2019

8.3K
Electrostatic Method to Remove Particulate Organic Matter from Soil
04:40

Electrostatic Method to Remove Particulate Organic Matter from Soil

Published on: February 10, 2021

5.2K

Related Experiment Videos

Last Updated: Jan 21, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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

Published on: June 20, 2025

1.2K
Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16
06:03

Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16

Published on: July 15, 2019

8.3K
Electrostatic Method to Remove Particulate Organic Matter from Soil
04:40

Electrostatic Method to Remove Particulate Organic Matter from Soil

Published on: February 10, 2021

5.2K

Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Drug discovery

Background:

  • Precise molecular interaction modeling is crucial for computational chemistry.
  • Accurate Hamiltonian and force field parameters are challenging for biomolecular systems.
  • Calculating interaction energies between different species, like protein-ligand complexes, is particularly difficult.

Purpose of the Study:

  • To evaluate the impact of different electrostatic models on ligand binding energy calculations during molecular docking.
  • To compare a classical Coulomb potential with a Poisson-Boltzmann (PB) model for electrostatic computations.
  • To assess the influence of these models on ligand pose prediction and virtual screening enrichment.

Main Methods:

  • Utilized DelPhi calculations for Poisson-Boltzmann (PB) electrostatic potential computation.
  • Compared PB model with a classical Coulomb potential with distance-dependent dielectrics.
  • Evaluated ligand docking performance using binding energies derived from both electrostatic models.
  • Investigated the combination of a smoothed Lennard-Jones potential with the PB model.

Main Results:

  • Electrostatic energies from Coulomb and PB models were highly correlated but differed significantly in magnitude (PB energies were ~10x smaller).
  • The Poisson-Boltzmann model led to improved ligand pose accuracy and better enrichment of true ligands over decoys compared to the Coulomb model.
  • A combination of the PB model with a smoothed Lennard-Jones potential provided a favorable balance between ligand sampling and scoring accuracy.

Conclusions:

  • The Poisson-Boltzmann model is superior to the classical Coulomb model for electrostatic calculations in ligand docking, reducing overestimation of polar interactions.
  • Accurate electrostatic modeling is critical for reliable prediction of ligand binding and virtual screening.
  • The PB model, particularly when combined with optimized van der Waals potentials, offers a robust approach for enhancing molecular docking and drug discovery efforts.