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

From: A comprehensive resource for integrating and displaying protein post-translational modifications

Features Previous PTM database[11] 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