PhosphoSitePlus

PhosphoSitePlus curates experimentally observed post-translational modifications (PTMs) on human and mouse proteins, providing site-level annotation and downloadable datasets for over 130,000 non-redundant modification sites including phosphorylation, ubiquitinylation, and acetylation.

Key Features:

• PTM catalog: Contains over 130,000 non-redundant modification sites annotated for phosphorylation, ubiquitinylation, and acetylation.
• Species focus: Site-level annotation concentrated on human and mouse proteins.
• Filtering by biological context: Search and dataset categorization by disease, tissue type, cell line, treatment, protein type, domain, cellular component, cell type, sequence, and motif.
• High-throughput dataset organization: High-throughput datasets are categorized by the biological and experimental parameters above.
• Site and protein annotations: Site-specific pages provide sequences, domain diagrams, molecular visualizations of modified side-chains, and descriptions of effects on protein function and cellular processes.
• Downloadable datasets: Modification sites and kinase–substrate datasets are available for download and network analysis.
• Sequence analysis tools: Includes sequence logo generators for motif analysis.
• Pathway and network export: Provides a Cytoscape plugin for kinase–substrate pathway visualization and downloadable BioPAX files for pathway analysis.
• Molecular visualization scripts: Provides downloadable PyMOL and Chimera scripts to colorize reactive groups on modified residues for structural studies.

Scientific Applications:

• PTM mapping and annotation: Curates experimentally observed modification sites for use in proteomics and PTM studies.
• Kinase–substrate network analysis: Supports construction and visualization of kinase–substrate interaction networks using downloadable datasets and a Cytoscape plugin.
• Pathway analysis: Enables pathway-level analyses via BioPAX exports.
• Structural interpretation: Supports structural studies of modified residues using PyMOL and Chimera scripts that colorize reactive groups.
• Motif discovery: Facilitates motif and sequence-context analysis of modification sites using sequence logo generation.

Methodology:

Provides sequence logo generation, a Cytoscape plugin for kinase–substrate pathway visualization, downloadable BioPAX files, downloadable PyMOL and Chimera scripts for colorizing modified residues, and downloadable modification site and kinase–substrate datasets.