Phospho.ELM: a database of phosphorylation sites--update 2011

Area of Science:

• Biochemistry
• Molecular Biology
• Bioinformatics

Background:

• Protein phosphorylation is a critical post-translational modification regulating cellular processes.
• Existing databases often lack comprehensive, integrated data on phosphorylation sites.
• The Phospho.ELM resource has been a key repository for phosphorylation data for over seven years.

Purpose of the Study:

• To present the updated Phospho.ELM database with new features and expanded content.
• To improve the utility of the database for researchers studying protein phosphorylation.
• To enhance data accessibility and integration with other biological resources.

Main Methods:

• Extraction of in vivo and in vitro phosphorylation data from scientific literature and phosphoproteomic studies.
• Implementation of new features including structural disorder/order, accessibility, and conservation scores.
• Development of visualization tools for phosphosite conservation on multiple sequence alignments.
• Integration with external databases and interaction networks.

Main Results:

• The database now contains 42,574 non-redundant phosphorylation sites (serine, threonine, tyrosine).
• New features provide insights into the structural context and evolutionary conservation of phosphorylation sites.
• Enhanced linking capabilities facilitate exploration of phosphosites within broader biological networks.

Conclusions:

• The updated Phospho.ELM database serves as a valuable, comprehensive resource for phosphorylation research.
• The new features enhance the ability to analyze and interpret phosphorylation site data.
• Improved integration promotes a systems-level understanding of phosphorylation in biological systems.