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

"Soft docking": matching of molecular surface cubes.

F Jiang1, S H Kim

  • 1Graduate Goup in Biophysics, University of California, Berkeley 94720.

Journal of Molecular Biology
|May 5, 1991
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

Clinical and radiological distinctiveness of anti-cyclic citrullinated peptide antibody-negative rheumatoid arthritis-associated interstitial lung disease: a retrospective cohort study.

Scandinavian journal of rheumatology·2026
Same author

[Risk assessment of subsequent drug resistance in patients with chemoresistant gestational trophoblastic neoplasia].

Zhonghua fu chan ke za zhi·2026
Same author

[Current advances and challenges of immunotherapy in gestational trophoblastic neoplasia].

Zhonghua yi xue za zhi·2026
Same author

[Association between cosleeping and emotional-behavioral problems and its differences with or without sleep anxiety in preschool children].

Zhonghua er ke za zhi = Chinese journal of pediatrics·2026
Same author

Fluorescent PSMA-Targeted Radiotheranostic Compounds for Multiscale Imaging.

Bioconjugate chemistry·2025
Same author

Efficacy and safety of biweekly single-dose actinomycin D versus multiday methotrexate in low-risk gestational trophoblastic neoplasia: a prospective multicenter randomized trial.

Annals of oncology : official journal of the European Society for Medical Oncology·2025

This study introduces a new molecular docking method using a "cube representation" to predict interaction sites between molecules. The technique effectively identifies correct molecular complexes, even with conformational changes, advancing computational drug discovery.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Biophysics

Background:

  • Molecular recognition is crucial for biological processes.
  • Understanding molecular interactions requires predicting binding sites.
  • Existing methods often struggle with conformational changes.

Purpose of the Study:

  • To develop a novel molecular docking method for predicting interaction sites.
  • To implicitly account for conformational changes during complex formation.
  • To provide a robust tool for analyzing molecular recognition.

Main Methods:

  • Developed a "cube representation" of molecular surfaces and volumes.
  • Implemented a two-stage docking procedure: geometric soft docking followed by energetic screening.

Related Experiment Videos

  • Tested the method on known molecular complexes from the Protein Data Bank (PDB).

    • Main Results:

    • The geometric docking stage successfully identified correct docking solutions in ideal cases.
    • The cube representation did not hinder the docking process.
    • The method demonstrated capability in accommodating conformational changes in realistic docking experiments.

    Conclusions:

    • The developed molecular docking method is effective in predicting interaction sites.
    • The approach implicitly handles conformational changes, enhancing accuracy.
    • This method offers a valuable tool for structural and computational biology research.