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

Rapid atomic density methods for molecular shape characterization.

J C Mitchell1, R Kerr, L F Ten Eyck

  • 1San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA, USA. mitchell@sdsc.edu

Journal of Molecular Graphics & Modelling
|July 14, 2001
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

Impact of tumor and node stages on the efficacy of adjuvant oxaliplatin-based chemotherapy in stage III colon cancer patients: an ACCENT pooled analysis.

ESMO open·2025
Same author

Responsible governance of genomics data and biospecimens in the context of broad consent: experiences of a pioneering access committee in Africa.

BMJ global health·2025
Same author

Different prognostic values of KRAS exon 2 submutations and BRAF V600E mutation in microsatellite stable (MSS) and unstable (MSI) stage III colon cancer: an ACCENT/IDEA pooled analysis of seven trials.

Annals of oncology : official journal of the European Society for Medical Oncology·2023
Same author

CXD101 and nivolumab in patients with metastatic microsatellite-stable colorectal cancer (CAROSELL): a multicentre, open-label, single-arm, phase II trial.

ESMO open·2022
Same author

Amoebic crab disease (ACD) in edible crab Cancer pagurus from the English Channel, UK.

Diseases of aquatic organisms·2022
Same author

Microbiomics: The Next Pillar of Precision Medicine and Its Role in African Healthcare.

Frontiers in genetics·2022
Same journal

Halide-encapsulated C<sub>24</sub> fullerenes as molecular redox hosts for alkali metals: A density functional theory study.

Journal of molecular graphics & modelling·2026
Same journal

Efficacy of Tinospora cordifolia bioactives as agonists of Smoothened (Smo) receptor to promote oligodendroglial lineage induction for remyelination-based therapy.

Journal of molecular graphics & modelling·2026
Same journal

Dynamic remodeling of USP28 by the selective inhibitor CAS-010: Insights from DFT and molecular dynamics simulations.

Journal of molecular graphics & modelling·2026
Same journal

Beyond the catalytic site: Voxilaprevir and Pasireotide as repurposed therapeutics for conformational inhibition of ADAR1.

Journal of molecular graphics & modelling·2026
Same journal

A mechanism-guided framework for prioritizing membrane-interaction anti-Vibrio peptides from peptidomics data.

Journal of molecular graphics & modelling·2026
Same journal

A multi-Level Study of 20S proteasome inhibitors: an integrated approach combining chemistry and Modelling.

Journal of molecular graphics & modelling·2026
See all related articles

Two novel methods, Fast Atomic Density Evaluation (FADE) and Pairwise Atomic Density Reverse Engineering (PADRE), rapidly characterize molecular shape using atomic density. These techniques identify surface features and assess shape complementarity for molecular docking.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Biophysics

Background:

  • Accurate molecular shape characterization is crucial for understanding molecular interactions.
  • Existing methods often define shape relative to a fixed surface, limiting local geometric analysis.

Purpose of the Study:

  • To introduce two new, rapid algorithms for molecular shape characterization.
  • To enable detailed analysis of local molecular geometry, including crevices and protrusions.
  • To facilitate the assessment of shape complementarity in molecular docking.

Main Methods:

  • Fast Atomic Density Evaluation (FADE) algorithm utilizing fast Fourier transforms for density estimation.
  • Pairwise Atomic Density Reverse Engineering (PADRE) method deriving density measures from atomic density and potential relationships.

Related Experiment Videos

  • Development of descriptors that measure local geometry from points within 3D space around a molecule.

    • Main Results:

    • FADE and PADRE provide rapid and efficient characterization of molecular shape.
    • The methods successfully identify and quantify local geometric features like crevices and protrusions.
    • Descriptors generated by FADE and PADRE are effective for testing shape complementarity.

    Conclusions:

    • FADE and PADRE offer advanced tools for molecular shape analysis.
    • These methods enhance the understanding of molecular surface topography.
    • The techniques are valuable for improving the accuracy of molecular docking predictions.