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

PoPS: a computational tool for modeling and predicting protease specificity.

Sarah E Boyd1, Maria Garcia de la Banda, Robert N Pike

  • 1School of Computer Science and Software Engineering and Victorian Bioinformatics Consortium, Monash University, Melbourne, Australia. sboyd@csse.monash.edu.au

Proceedings. IEEE Computational Systems Bioinformatics Conference
|February 2, 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

Discordance Between Systemic Lupus Erythematosus Disease Activity Index Domain Weights and Their Association With Organ Damage Accrual.

Arthritis care & research·2026
Same author

<i>Helicobacter pylori</i> induces the production of interleukin-37 to promote broad immunosuppression and enhance colonization.

Gut microbes·2026
Same author

Characteristics of T-Cells Expressing IL-37 and Its Receptors in Inflammatory Bowel Disease.

International journal of molecular sciences·2026
Same author

Structural basis for uPAR binding to an antibody developed for targeted cancer therapy. Mechanistic insights into flexibility, ligand recognition, and molecular imaging.

Protein science : a publication of the Protein Society·2026
Same author

The crystal structure of the toxin EspC from enteropathogenic <i>Escherichia coli</i> reveals the mechanism that governs host cell entry and cytotoxicity.

Gut microbes·2025
Same author

PhiSiCal-Checkup: A Bayesian framework to validate amino acid conformations within experimental protein structures.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same journal

A Two-Step Approach for Clustering Proteins based on Protein Interaction Profile.

Proceedings. IEEE Computational Systems Bioinformatics Conference·2008
Same journal

Proceedings of 2005 IEEE Computational Systems Bioinformatics Conference. August 8-11, 2005. Stanford, California, USA.

Proceedings. IEEE Computational Systems Bioinformatics Conference·2007
Same journal

Fractal genomics modeling: a new approach to genomic analysis and biomarker discovery.

Proceedings. IEEE Computational Systems Bioinformatics Conference·2006
Same journal

Gene Ontology friendly biclustering of expression profiles.

Proceedings. IEEE Computational Systems Bioinformatics Conference·2006
Same journal

Comparative analysis of gene sets in the Gene Ontology space under the multiple hypothesis testing framework.

Proceedings. IEEE Computational Systems Bioinformatics Conference·2006
Same journal

AZuRE, a scalable system for automated term disambiguation of gene and protein names.

Proceedings. IEEE Computational Systems Bioinformatics Conference·2006
See all related articles

Identifying protease cleavage sites is challenging. The PoPS bioinformatics tool offers a novel method for building computational models of protease specificity, improving prediction accuracy for substrates and proteomes.

Area of Science:

  • Biochemistry and Bioinformatics
  • Molecular Biology
  • Proteomics

Background:

  • Proteases are crucial enzymes regulating cellular processes through specific amino acid sequence cleavage.
  • Current computational methods for predicting protease cleavage sites are limited by pattern-based or frequency matrix approaches.
  • Accurate identification of protease targets remains a significant challenge in biological research.

Purpose of the Study:

  • To introduce PoPS, a novel bioinformatics tool for developing computational models of protease specificity.
  • To provide a flexible platform for building protease specificity models using diverse experimental data or expert knowledge.
  • To enable accurate prediction and ranking of protease cleavage sites in substrates and proteomes.

Main Methods:

Related Experiment Videos

  • Development of the PoPS (Protease Specificity) bioinformatics tool.
  • Utilizing amino acid sequences as a basis for specificity models.
  • Incorporating experimental data or expert knowledge for model construction.
  • Leveraging substrate secondary and tertiary structures for enhanced prediction accuracy.

    • Main Results:

    • PoPS offers a novel approach to modeling protease specificity beyond traditional sequence patterns.
    • The tool enables prediction and ranking of likely cleavage events within individual substrates.
    • PoPS facilitates the analysis of protease activity across entire proteomes.
    • The system supports model inference, comparison, testing, and storage in a public database.

    Conclusions:

    • PoPS provides a powerful and flexible bioinformatics solution for predicting protease cleavage sites.
    • The tool enhances the understanding of protease function and substrate interactions.
    • PoPS is a valuable resource for researchers in proteomics and molecular biology, accessible via a public web server.