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 Experiment Videos

Computer simulation of the receptor-ligand system.

Piotr Romiszowski1, Andrzej Sikorski

  • 1Department of Chemistry, University of Warsaw, 1 Pasteura Str., 02-093 Warsaw, Poland. prom@chem.uw.edu.pl

Acta Poloniae Pharmaceutica
|April 3, 2003
PubMed
Summary

This study simulated receptor-ligand docking using a simplified model, finding it effective for identifying binding sites and ligand orientation. The Monte Carlo simulations explored complex stability with statistical potentials.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Self-Diffusion in Two-Dimensional Colloidal Systems: A Computer Simulation Study.

Entropy (Basel, Switzerland)·2025
Same author

Serum Iodine Levels and 8-Year Survival in Patients After Kidney Cancer Diagnosis.

Cancers·2025
Same author

Liquid dynamics in a crowded environment: Bond percolation vs site percolation.

Chaos (Woodbury, N.Y.)·2025
Same author

Monte Carlo Simulations of Polymer Collapse in an Explicit Solvent of Varying Quality.

Polymers·2025
Same author

Simulation Studies of Dynamical Heterogeneity in a Dense Two-Dimensional Dimer-Solvent System with Obstacles.

Entropy (Basel, Switzerland)·2025
Same author

The Kinetics of Polymer Brush Growth in the Frame of the Reaction Diffusion Front Formalism.

Polymers·2024

Area of Science:

  • Computational chemistry and structural biology.
  • Molecular modeling and simulation.

Background:

  • Accurate modeling of receptor-ligand interactions is crucial for drug discovery.
  • Simplified models are needed to reduce computational cost in molecular docking.

Purpose of the Study:

  • To develop and validate a simplified low-resolution model for receptor-ligand docking simulations.
  • To assess the model's ability to predict binding sites and ligand orientation.
  • To investigate the stability of protein-ligand complexes using statistical potentials.

Main Methods:

  • Monte Carlo simulations were performed on receptor-ligand systems from the Protein Data Bank.
  • Simplified models used alpha carbons and united atoms for side groups.
  • Excluded volume and pairwise contact potentials were incorporated.

Related Experiment Videos

  • Ligand docking was simulated via random translations and reorientations.

    • Main Results:

    • The simplified model successfully identified binding sites on receptor surfaces.
    • Proper orientation of docked ligands was predicted.
    • The stability of formed complexes was evaluated using statistical potentials.
    • The model demonstrated feasibility for predicting docking outcomes.

    Conclusions:

    • A low-resolution Monte Carlo simulation approach is feasible for receptor-ligand docking.
    • The simplified model can accurately predict binding sites and ligand orientation.
    • This method offers a computationally efficient approach for studying molecular interactions.