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

PDZBase: a protein-protein interaction database for PDZ-domains.

Thijs Beuming1, Lucy Skrabanek, Masha Y Niv

  • 1Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Ave., New York, NY 10021, USA.

Bioinformatics (Oxford, England)
|October 30, 2004
PubMed
Summary

PDZBase is a new database cataloging PDZ-domain protein-protein interactions. It offers sequence and keyword searches, aiding research into these crucial molecular connections.

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

Many ligands and states of bitter taste GPCRs.

Nature structural & molecular biology·2026
Same author

Intracellular and dual-site inhibition of a bitter taste GPCR.

Cellular and molecular life sciences : CMLS·2026
Same author

Effects of the genetic polymorphisms of TAS2R43 and TAS2R46 on receptors' function and on perceived bitterness of caffeine by human subjects.

Chemical senses·2025
Same author

Recognition of Specific PIP2-subtype Composition Triggers the Allosteric Control Mechanism for Selective Membrane Targeting of Cargo Loading and Release Functions of the Intracellular Sterol Transporter StarD4.

Journal of molecular biology·2025
Same author

A bio. tools collection of online resources for GPCR research.

British journal of pharmacology·2025
Same author

Increasing the Efficiency of Ensemble Molecular Dynamics Simulations with Termination of Unproductive Trajectories Identified at Runtime.

The journal of physical chemistry. A·2025

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Structural Biology

Background:

  • PDZ domains are crucial protein interaction modules involved in various cellular processes.
  • Understanding PDZ-domain-mediated interactions is vital for deciphering cellular signaling pathways.
  • A comprehensive resource for these interactions is currently lacking.

Purpose of the Study:

  • To create PDZBase, a centralized database of PDZ-domain-mediated protein-protein interactions.
  • To facilitate the study and analysis of PDZ domain functions and interactions.

Main Methods:

  • Manual curation of protein-protein interactions from over 200 scientific articles.
  • Development of a searchable database structure for PDZ interactions.
  • Implementation of sequence motif and keyword-based search functionalities.

Related Experiment Videos

Main Results:

  • PDZBase currently contains approximately 300 manually curated PDZ-domain-mediated interactions.
  • The database allows for flexible querying using sequence motifs and keywords.
  • Interactive visualization tools, including sequence alignments and residue-based diagrams with secondary structure information, are available.

Conclusions:

  • PDZBase serves as a valuable, comprehensive resource for PDZ-domain interactions.
  • The database enhances the accessibility and analysis of protein-protein interaction data.
  • PDZBase will aid researchers in investigating the roles of PDZ domains in biological systems.