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

Limitations of atom-centered dielectric functions in implicit solvent models.

Jessica M J Swanson, John Mongan, J Andrew McCammon

    The Journal of Physical Chemistry. B
    |July 21, 2006
    PubMed
    Summary

    Atom-centered surfaces in implicit solvent models create artificial high dielectric regions. Excluding these interstitial pockets is crucial for accurate solvation energy and nonbonded interaction calculations in proteins.

    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

    A small molecule reduces both parkinsonism and l-dopa-induced dyskinesia in animal models of Parkinson's disease.

    Science translational medicine·2026
    Same author

    Structure and dynamics in drug discovery.

    npj drug discovery·2026
    Same author

    The scientific legacy of Martin Karplus from the perspective of his collaborators.

    Biophysical journal·2026
    Same author

    Markovian state models uncover casein kinase 1 dynamics that govern circadian period.

    Biophysical journal·2025
    Same author

    The need to implement FAIR principles in biomolecular simulations.

    Nature methods·2025
    Same author

    Markovian State Models uncover Casein Kinase 1 dynamics that govern circadian period.

    bioRxiv : the preprint server for biology·2025

    Area of Science:

    • Computational chemistry
    • Biophysics
    • Molecular modeling

    Background:

    • Implicit solvent models like Poisson-Boltzmann and generalized Born are vital in computational chemistry.
    • These models often define dielectric boundaries using atom-centered functions.
    • Existing methods contrast with the Lee and Richards molecular surface definition.

    Discussion:

    • Atom-centered surfaces create small, unfillable interatomic crevices and buried pockets.
    • These interstitial regions possess a high dielectric constant.
    • Their presence is significant in globular proteins, leading to inaccuracies.

    Key Insights:

    • Interstitial high dielectric regions artificially inflate solvation energies.
    • These regions distort the free energy surface of nonbonded interactions.

    Related Experiment Videos

  • Accurate physical modeling requires excluding these pockets from dielectric functions.

    • Outlook:

    • Future implicit solvent models should incorporate methods to exclude interstitial high dielectric regions.
    • This refinement will improve the physical realism of molecular simulations.
    • Enhanced accuracy in solvation energy and interaction free energies is anticipated.