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

Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities

E C Meng1, I D Kuntz, D J Abraham

  • 1Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143-0446.

Journal of Computer-Aided Molecular Design
|June 1, 1994
PubMed
Summary

This study shows atomic hydrophobicities can effectively score ligand-receptor binding modes. The Hydropathic INTeractions (HINT) function accurately predicted the correct binding orientation in most tested molecular docking simulations.

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 CONTRIBUTION TO THE UNDERSTANDING OF THE PRIMARY QUANTUM CONVERSION IN PHOTOSYNTHESIS. UCRL-11212.

UCRL [reports]. U.S. Atomic Energy Commission·2014
Same author

Fabrication and characterization of bioactive composite coatings on Mg-Zn-Ca alloy by MAO/sol-gel.

Journal of materials science. Materials in medicine·2011
Same author

Multiplex immune serum biomarker profiling in sarcoidosis and systemic sclerosis.

The European respiratory journal·2009
Same author

Overview of pathogenesis of systemic sclerosis.

Rheumatology (Oxford, England)·2009
Same author

Endothelin receptor selectivity: evidence from in vitro and pre-clinical models of scleroderma.

European journal of clinical investigation·2009
Same author

Connective tissue growth factor (CTGF, CCN2) gene regulation: a potent clinical bio-marker of fibroproliferative disease?

Journal of cell communication and signaling·2009

Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Drug discovery

Background:

  • Predicting ligand-receptor binding geometries is crucial for discovering new drugs.
  • Understanding binding complementarity factors aids in rational drug design.

Purpose of the Study:

  • To evaluate the utility of atomic hydrophobicities in assessing ligand-receptor binding modes.
  • To determine if the HINT (Hydropathic INTeractions) function can serve as a reliable scoring method in molecular docking.

Main Methods:

  • Generated hundreds of hypothetical binding orientations for four known ligand-receptor complexes using DOCK.
  • Evaluated these orientations using the HINT exponential function and atomic hydrophobic constants.

Main Results:

Related Experiment Videos

  • The experimental binding mode achieved the best HINT score in three out of four systems.
  • In the remaining system, the experimental binding mode scored only slightly lower than a plausible alternative orientation.

Conclusions:

  • Atomic hydrophobicities, particularly via the HINT function, show promise as a scoring method in molecular docking.
  • This approach can aid in identifying correct ligand-receptor binding geometries and facilitate ligand discovery.