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PhosphoBase: a database of phosphorylation sites
N Blom1, A Kreegipuu, S Brunak
1Center for Biological Sequence Analysis, Department of Chemistry, Building 207, The Technical University of Denmark, DK-2800 Lyngby, Denmark. nikob@cbs.dtu.dk
Nucleic Acids Research
|February 21, 1998
Summary
PhosphoBase is a new database detailing experimentally verified phosphorylation sites. It compiles data from literature and protein databases, offering insights into phosphoproteins and kinase activity.
Area of Science:
- Biochemistry
- Molecular Biology
- Bioinformatics
Background:
- Phosphorylation is a key post-translational modification regulating protein function.
- A centralized resource for experimentally verified phosphorylation sites is needed.
- Existing databases may lack comprehensive kinetic and positional data.
Purpose of the Study:
- To introduce PhosphoBase, a curated database of phosphorylation sites.
- To provide detailed information on phosphoproteins, site locations, and associated kinetic data.
- To demonstrate the utility of the database through a PKA substrate analysis.
Main Methods:
- Compilation and revision of data from scientific literature.
- Integration of information from major protein sequence databases (SwissProt, PIR).
- Development of a web-accessible database (PhosphoBase).
Main Results:
- PhosphoBase version 1.0 contains 156 entries and 398 experimentally determined phosphorylation sites.
- Entries include phosphoprotein details, precise phosphorylation site positions.
- Some entries incorporate kinetic data from enzyme assays on specific peptides.
Conclusions:
- PhosphoBase serves as a valuable resource for researchers studying protein phosphorylation.
- The database facilitates the study of phosphorylation site conservation and kinase specificity.
- Accessible online, PhosphoBase supports advancements in molecular biology and drug discovery.