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

Protein secondary structure assignment through Voronoï tessellation.

Franck Dupuis1, Jean-François Sadoc, Jean-Paul Mornon

  • 1Laboratoire de Minéralogie Cristallographie Paris, CNRS UMR 7590, Universités Paris 6 et 7, Paris, France.

Proteins
|April 23, 2004
PubMed
Summary

We introduce VoTAP, a novel algorithm for assigning polypeptide secondary structures using alpha-carbon coordinates and Voronoi tessellation. This method enhances accuracy by analyzing residue contacts, improving protein structure prediction.

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

Mechanistic Insights into Cystic Fibrosis Transmembrane Conductance Regulator Function from Molecular Dynamics Analysis of Electrostatic Interactions.

Journal of chemical information and modeling·2026
Same author

CFTR correctors potentiate gating mutants causing cystic fibrosis.

Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society·2025
Same author

Hydrophobic cluster analysis at protein and proteome scales.

Biochimie·2025
Same author

Novel gain-of-function mutants identify a critical region within CFTR membrane-spanning domain 2 controlling cAMP-dependent and ATP-independent channel activation.

Cellular and molecular life sciences : CMLS·2024
Same author

Acting on the CFTR Membrane-Spanning Domains Interface Rescues Some Misfolded Mutants.

International journal of molecular sciences·2022
Same author

Digging into the 3D Structure Predictions of AlphaFold2 with Low Confidence: Disorder and Beyond.

Biomolecules·2022

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Biophysics

Background:

  • Accurate secondary structure assignment is crucial for understanding protein function.
  • Existing automatic methods have limitations in precision and handling of complex structures.

Purpose of the Study:

  • To develop a new, accurate, and automated algorithm for secondary structure assignment.
  • To leverage geometric principles for improved residue contact definition and analysis.

Main Methods:

  • Utilized three-dimensional Voronoi tessellation to define residue contacts based on alpha-carbon coordinates.
  • Developed a two-stage assignment process: initial assignment using low-order contacts, followed by strand assignment using distant residue contacts.
  • Trained and validated the algorithm on a dataset of 282 well-refined protein structures.

Related Experiment Videos

Main Results:

  • VoTAP effectively assigns secondary structures by analyzing novel contact matrices derived from Voronoi polyhedra.
  • The algorithm distinguishes between strong and normal low-order contacts, refining assignment accuracy.
  • Performance comparisons demonstrate competitive or superior results compared to existing automatic methods, with an investigation into resolution's influence.

Conclusions:

  • VoTAP offers a robust and accurate method for automated secondary structure assignment.
  • The geometric approach provides a novel way to define and interpret residue interactions.
  • This algorithm has the potential to advance protein structure analysis and prediction.