PTMCode

PTMCode maps and catalogs functional associations between protein post-translational modifications (PTMs) within and across interacting proteins to support analysis of PTM-mediated regulation.

Key Features:

• Extensive database: Contains data on 316,546 modified sites across 69 PTM types, propagated through orthologs among 19 eukaryotic species to yield over 1.6 million sites and more than 17 million functional associations involving over 100,000 proteins.
• Evidence-based associations: Compiles PTM associations based on five evidence channels: literature survey, residue co-evolution, structural proximity, co-occurrence of PTMs at the same residue, and location within PTM-enriched protein regions (hotspots).
• Cross-species analysis: Includes PTM data propagated across 19 eukaryotic species to enable comparative analyses of conserved and divergent PTM patterns.
• High-throughput PTM mapping: Incorporates PTM site data derived from high-throughput technologies to assemble a large-scale dataset of modified residues.
• Residue and protein coverage: Covers nearly 75,000 annotated residues across more than 10,000 proteins for analysis of site-specific and protein-level PTM interactions.

Scientific Applications:

• Combinatorial PTM code analysis: Enables study of combinations of PTMs on proteins to investigate how distinct PTM patterns modulate cellular functions.
• Identification of regulatory mechanisms: Supports identification of potential regulatory PTM interactions and hypotheses about their functional roles.
• Structural implication studies: Facilitates analysis of how PTMs affect protein stability and interactions via structural proximity evidence.
• Evolutionary investigations: Enables investigation of evolutionary conservation and divergence of PTM patterns across eukaryotic species.

Methodology:

PTMCode compiles and integrates PTM associations from five explicit evidence channels (literature survey; residue co-evolution; structural proximity; co-occurrence at the same residue; location within PTM-enriched hotspots), propagates PTM annotations through orthologs across 19 eukaryotic species, and incorporates PTM site data derived from high-throughput mapping technologies.