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

Search for structural similarity in proteins.

Jacek Leluk1, Leszek Konieczny, Irena Roterman

  • 1Institute of Biochemistry and Molecular Biology University of Wrocław, Tamka 2, Poland. lulu@bf.uni.wroc.pl

Bioinformatics (Oxford, England)
|December 25, 2002
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

Life - A glimpse into the phenomenon.

Bioinformation·2026
Same author

Chameleon sequences reveal structural effects in proteins representing micelle-like distribution of hydrophobicity.

FEBS open bio·2026
Same author

Activity of Serpins in Context to Hydrophobic Interaction.

Biomolecules·2025
Same author

Heat Shock Protein and Disaggregase Influencing the Casein Structuralisation.

International journal of molecular sciences·2025
Same author

Chameleon sequences-Structural effects.

PloS one·2025
Same author

Aquaporins as Membrane Proteins: The Current Status.

Frontiers in bioscience (Scholar edition)·2025

A new method, VeaR (V-angle and radius of curvature), uses geometric parameters to rapidly assess protein structural similarity. This approach offers a distinct criterion for protein comparison beyond sequence homology.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Protein sequence and structure databases are rapidly expanding, necessitating efficient similarity search methods.
  • Existing methods may not fully capture the nuances of protein structural relationships.

Purpose of the Study:

  • To introduce and evaluate a novel method, VeaR (V-angle and radius of curvature), for rapid protein structural similarity searching.
  • To explore the utility of geometric parameters in protein structural comparison.

Main Methods:

  • Utilized dihedral angle (V) and radius of curvature (R) of pentapeptide fragments as geometric parameters.
  • Analyzed the dependence of R on V in model polypeptides and real protein structures.
  • Compared VeaR structural comparison with sequence similarity analysis using the genetic semihomology algorithm.

Related Experiment Videos

Main Results:

  • The parabolic function relating R and V, characteristic of model polypeptides, is altered in real proteins.
  • This alteration forms a characteristic pattern for individual proteins, usable as a similarity criterion.
  • VeaR demonstrated effectiveness in structural comparison across a diverse range of protein structures.

Conclusions:

  • VeaR provides a novel and effective criterion for judging protein structural similarity.
  • Geometric parameters offer a complementary approach to sequence-based methods for protein comparison.
  • The concept of 'consensus structure' is introduced, analogous to 'consensus sequence', for protein families like serpine.