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

Fast similarity search for protein 3D structures using topological pattern matching based on spatial relations.

Sung-Hee Park1, Keun Ho Ryu, David Gilbert

  • 1Database Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, 361-763, Korea. shpark@dblab.chungbuk.ac.kr

International Journal of Neural Systems
|September 28, 2005
PubMed
Summary

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

Breast Cancer in Transgender Patients Following Medical and Surgical Intervention.

Clinical breast cancer·2026
Same author

Efficacy of home-based low-level laser therapy in patients with low back pain: a double-blinded randomized controlled trial.

Lasers in medical science·2026
Same author

Transformer-based feature extraction approach for hematopoietic cancer subtype classification.

Computers in biology and medicine·2026
Same author

Synergistic effects of ultrasound combined with aqueous chlorine dioxide on the reduction of <i>Yersinia enterocolitica</i> in leaf mustard (<i>Brassica juncea</i>).

Food science and technology international = Ciencia y tecnologia de los alimentos internacional·2026
Same author

Objective motor function assessment using diffusion tensor tractography in subacute acquired brain injury: A retrospective observational study.

Medicine·2025
Same author

The concept of the digital therapeutic garden and its psychological effects.

Frontiers in psychology·2025

This study introduces a faster method for protein 3D structure similarity searching by representing structures as spatial objects and using topological patterns. This approach significantly improves search speed for large protein databases.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Database Systems

Background:

  • Protein 3D structure databases are growing rapidly, making similarity searches computationally expensive and slow.
  • Existing comparison systems often lack the speed required for practical applications like protein structure classification.

Purpose of the Study:

  • To develop a fast and efficient system for protein 3D structure similarity searching.
  • To address the limitations of current methods in terms of speed and scalability.

Main Methods:

  • A multi-step processing approach involving preprocessing, filtering, and refinement.
  • Representing protein structures as spatial objects using geometric properties.
  • Employing approximate topological string matching for efficient candidate set generation.

Related Experiment Videos

  • Utilizing spatial relations of secondary structure elements for pattern discovery.

    • Main Results:

    • The developed system demonstrates a significant advantage in speed compared to existing methods like DALI.
    • The approach using topological relations of secondary structure elements is practical for fast similarity searches.
    • The system is fully implemented using Oracle 8i spatial.

    Conclusions:

    • The proposed method offers a practical and efficient solution for fast protein 3D structure similarity searching.
    • Leveraging spatial databases and topological pattern discovery enhances search performance.
    • This approach is suitable for large-scale protein structure classification tasks.