dbPTM

dbPTM catalogs and annotates protein post-translational modification (PTM) sites—including phosphorylation, glycosylation, and sulfation—by integrating experimentally validated sites and providing structural and functional context for PTM analysis.

Key Features:

• PTM coverage: Curates phosphorylation, glycosylation, and sulfation sites as the primary PTM types.
• Data integration: Integrates experimentally validated PTM sites from Swiss-Prot, PhosphoELM, and O-GLYCBASE.
• Systematic identification: Identifies PTM sites within the context of Swiss-Prot proteins.
• Prediction refinement: Refines the KinasePhos prediction tool for site identification.
• Structural annotations: Provides solvent accessibility and secondary structure predictions for residues at PTM sites.
• Functional context: Includes protein domain annotations and sequence variations associated with PTM sites.

Scientific Applications:

• Protein function and regulation: Enables analysis of how PTMs influence protein function and regulatory mechanisms.
• Structural context analysis: Supports interpretation of PTMs in relation to solvent accessibility and secondary structure.
• Mechanism and interaction studies: Facilitates elucidation of mechanisms underlying protein activity and protein–protein interactions mediated by PTMs.

Methodology:

Integrates experimentally validated PTM sites from Swiss-Prot, PhosphoELM, and O-GLYCBASE, systematically maps PTM sites to Swiss-Prot proteins, refines the KinasePhos prediction method, and computes solvent accessibility and secondary structure predictions for modified residues.