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

Revisiting Partition in Hydrated Bilayer Systems.

João T S Coimbra1, Pedro A Fernandes1, Maria J Ramos1

  • 1UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.

Journal of Chemical Theory and Computation
|April 8, 2017
PubMed
Summary
This summary is machine-generated.

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

Binding Mechanism of UAMC-1110 to Fibroblast Activation Protein.

Journal of chemical information and modeling·2026
Same author

Mechanism of Polyester Hydrolysis by Marine Bacterium PE-H Enzyme: an Atomistic and Thermodynamic Characterization.

Journal of chemical information and modeling·2026
Same author

Mechanism of Hyaluronic Acid Hydrolysis Catalyzed by Snake Venom Hyaluronidase.

Journal of chemical information and modeling·2026
Same author

Revealing the rationale behind the differential neutralization of phospholipase A<sub>2</sub> (PLA<sub>2</sub>) enzymes in snake and bee venom by varespladib (LY-315920), a small molecule PLA<sub>2</sub> inhibitor.

Journal of biomolecular structure & dynamics·2025
Same author

Off the beaten (catalytic) path: Charting the mechanistic space of enzyme reactions.

The Journal of chemical physics·2025
Same author

Molecular dynamics of Lys49 PLA<sub>2</sub>-like toxins: Insights into solution and membrane-bound conformations.

Toxicon : official journal of the International Society on Toxinology·2025

Potential-energy modification methods, like flooding, improve convergence in umbrella sampling simulations for drug permeation. These techniques enhance sampling and accurately describe molecular behavior during water-bilayer passage.

Area of Science:

  • Computational chemistry
  • Molecular dynamics simulations
  • Biomolecular simulations

Background:

  • Umbrella sampling simulations are crucial for studying permeation processes.
  • Generating appropriate starting structures is a challenge for simulation convergence.
  • Accurate simulation of drug-like compound permeation requires robust methodologies.

Purpose of the Study:

  • To address potential-of-mean force (PMF) convergence issues in umbrella sampling.
  • To evaluate potential-energy modification methods for enhancing sampling.
  • To improve the accuracy of simulating water-bilayer permeation for drug-like compounds.

Main Methods:

  • Utilized potential-energy modification techniques, specifically the flooding method.
  • Employed umbrella sampling simulations for water-bilayer permeation studies.

Related Experiment Videos

  • Incorporated atomic polarization and conformation-dependent atomic point charges.

    • Main Results:

    • Demonstrated that potential-energy modification enhances sampling and PMF convergence.
    • Showcased the ability of potential modifiers to introduce bias for accurate internal degree-of-freedom description.
    • Validated computed values against experimental data where applicable.

    Conclusions:

    • Potential-energy modification methods offer a viable solution for PMF convergence challenges.
    • These methods improve the accuracy of describing permeation processes for drug-like compounds.
    • Conformation-dependent atomic point charges significantly impact predicted PMF values.