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PhosphoBase, a database of phosphorylation sites: release 2.0
A Kreegipuu1, N Blom, S Brunak
1Institute of Chemical Physics, University of Tartu, 2 Jakobi St., EE2400 Tartu, Estonia.
Nucleic Acids Research
|December 10, 1998
Summary
PhosphoBase is a database detailing protein phosphorylation sites and kinase activity. It compiles data from scientific literature, offering insights into protein modification and kinase interactions.
Area of Science:
- Biochemistry
- Molecular Biology
- Bioinformatics
Background:
- Protein phosphorylation is a critical post-translational modification regulating cellular processes.
- Understanding phosphorylation patterns is essential for deciphering signal transduction pathways.
- Existing resources for phosphorylation data were limited in scope and accessibility.
Purpose of the Study:
- To create a comprehensive, literature-curated database of protein phosphorylation.
- To provide a centralized resource for researchers studying protein kinases and their substrates.
- To facilitate the study of phosphorylation site specificity and kinetics.
Main Methods:
- Systematic literature review to identify and extract phosphorylation data.
- Data compilation into a standardized format for consistent analysis.
- Cross-referencing database entries with established protein and literature databases (Swiss-Prot, MedLine).
Main Results:
- PhosphoBase version 2.0 (October 1998) contains 414 phosphoprotein entries.
- Includes 1052 identified phosphorylatable serine, threonine, and tyrosine residues.
- Incorporates kinetic data for approximately 330 oligopeptides from phosphorylation assays.
Conclusions:
- PhosphoBase serves as a valuable, integrated resource for protein phosphorylation research.
- The database enhances accessibility to curated phosphorylation site and kinase activity data.
- Facilitates further investigation into the roles of protein phosphorylation in biological systems.