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

Multipolar representation of protein structure.

Apostol Gramada1, Philip E Bourne

  • 1Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA. agramada@sdsc.edu

BMC Bioinformatics
|May 6, 2006
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

Deciphering covalent kinase inhibitor binding landscape through structural kinome profiling.

European journal of medicinal chemistry·2026
Same author

Governing real-world health data as a public utility.

Science (New York, N.Y.)·2026
Same author

AI-powered programmable virtual humans toward human physiologically-based drug discovery.

Drug discovery today·2025
Same author

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13.

Journal of chemical information and modeling·2025
Same author

Biological databases in the age of generative artificial intelligence.

Bioinformatics advances·2025
Same author

Exploring Extended Warheads toward Developing Cysteine-Targeted Covalent Kinase Inhibitors.

Journal of chemical information and modeling·2024

We developed a novel multipole-based protein representation that captures structural details for improved protein function analysis. This method offers a more granular and generalizable approach compared to traditional coordinate-based methods.

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Protein structure-function paradigm is central but limited.
  • Protein function relies on cooperative effects at residue scales.
  • Current atomic coordinate representations are inadequate for bridging structure and function.

Purpose of the Study:

  • To propose a new parameterization for protein structure and physicochemical properties.
  • To bridge the gap between atomic-level structure and protein-level functionality.
  • To develop a quantitative description of protein shape and enable comparisons at various detail levels.

Main Methods:

  • Utilized multipoles associated with residue Calpha coordinates as shape descriptors.
  • Developed a (dis)similarity measure in multipolar configuration space.

Related Experiment Videos

  • Tested the parameterization on the protein kinase-like superfamily benchmark set.

    • Main Results:

    • Demonstrated quantitative description and comparison of protein shapes using multipoles.
    • Showed robust discrimination between protein families, outperforming sequence/conventional methods.
    • Confirmed correlation with Cartesian coordinates increases with multipole rank (level of detail).

    Conclusions:

    • Achieved granular protein structure description using multipolar coefficients.
    • The multipole representation is generalizable to residue-specific properties.
    • Provides a unified framework for studying and comparing spatial profiles of protein properties.