PPS

PPS identifies known and potential post-translational modification (PTM) sites, focusing on phosphorylation in eukaryotic proteins by leveraging the Phospho.ELM database of experimentally verified phosphorylation sites.

Key Features:

• Comprehensive database: Leverages Phospho.ELM, a manually curated repository of phosphorylation sites compiled from published literature and high-throughput datasets.
• Extensive data coverage: References Phospho.ELM v7.0 entries covering 4,078 phospho-protein sequences with 12,025 phosphoserine, 2,362 phosphothreonine, and 2,083 phosphotyrosine sites.
• Detailed annotations: Provides annotated residue positions, reported responsible kinases where known, subcellular localization, tissue distribution, signaling pathway involvement, literature references, and links to molecular interaction databases such as MINT.
• Integration with external databases: Cross-references UniProt, PubMed, SMART, ELM, MSD, and protein interaction resources including STRING for extended annotation and evidence linking.
• Advanced search and sequence lookup: Supports keyword and UniProt accession searches and includes BLAST-based sequence queries to retrieve phosphorylated peptides from the curated dataset.

Scientific Applications:

• Phosphorylation site identification: Enables identification and retrieval of experimentally reported phosphorylation sites for proteins of interest.
• Regulatory residue analysis: Facilitates study of the regulatory roles of phosphoserine, phosphothreonine, and phosphotyrosine residues in cellular processes.
• Signaling pathway and kinase specificity research: Supports investigations into signaling pathways and kinase–substrate relationships using curated site and kinase annotation.
• Experimental design and computational modeling: Provides curated site data and annotations to inform experimental validation and computational models of phosphorylation-dependent regulation.

Methodology:

Integration of manually curated phosphorylation site data from Phospho.ELM with updates derived from published literature and high-throughput studies; entries include literature references and cross-database links.