Table 2 The enhanced features in this expanding PTM database (dbPTM 2.0).

Protein entry

UniProtKB/Swiss-Prot (release 46)

UniProtKB/Swiss-Prot (release 55)

Experimental PTM resource

UniProtKB/Swiss-Prot, Phospho.ELM, and O-GLYCBASE

UniProtKB/Swiss-Prot, Phospho.ELM, PHOSIDA, HPRD, O-GLYCBASE, and UbiProt

Computationally predicted PTMs

Phosphorylation, glycosylation, and sulfation

About 25 types of PTM (phosphorylation, glycosylation, sulfation, acetylation, methylation, sumoylation, hydroxylation, etc.)

Protein structure

Protein Data Bank (PDB)

Protein Data Bank (PDB)

PTM annotation

RESID (373 PTM annotations)

RESID (431 PTM annotations)

Structural investigation of PTM sites

-

Solvent accessibility, secondary structure and intrinsic disorder region

Kinase family annotation

-

KinBase

Protein domain

InterPro

InterPro

Protein variation

Swiss-Prot and Ensembl

Swiss-Prot and Ensembl

Site-specific PTM literature

-

Extracting the PTM-related literatures from UniProtKB/Swiss-Prot, Phospho.ELM, HPRD, O-GLYCBASE, and UbiProt

Substrate specificity

-

Amino acid frequency, solvent accessibility, secondary structure and disorder region surrounding modified sites

Evolutionary conservation of PTM sites

-

COG and ClustalW

PTM benchmark set for computational studies

-

Providing the benchmark for constructing PTM test set to compare the predictive performance of prediction tools

Relationship between PTM and subcellular localization

-

Analyzing the relationship between PTM and subcellular localization

Graphical visualization

PTM, solvent accessibility, secondary structure, protein variation, protein domain, and tertiary structure

PTM, solvent accessibility, secondary structure, protein variation, protein domain, tertiary structure, orthologous conserved regions, substrate site specificity and protein interaction network