dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications

Abstract

Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version. Due to the increasing number of studies on the mechanism of PTMs in the past few years, a great deal of upstream regulatory proteins of PTM substrate sites have been revealed. The updated dbPTM thus collates regulatory information from databases and literature, and merges them into a protein-protein interaction network. To enhance the understanding of the association between PTMs and molecular functions/cellular processes, the functional annotations of PTMs are curated and integrated into the database. In addition, the existing PTM-related resources, including annotation databases and prediction tools are also renewed. Overall, in this update, we would like to provide users with the most abundant data and comprehensive annotations on PTMs of proteins. The updated dbPTM is now freely accessible at https://awi.cuhk.edu.cn/dbPTM/.

Emerging Trends and Research Foci in Tumor Microenvironment of Pancreatic Cancer: A Bibliometric and Visualized Study

“…The research and application of targeted adjuvant therapy has attracted increasing attention from researchers ( 38 ). Studies have shown that glutaminolysis can be controlled by glutaminase succinylation, leading to the inhibition of tumor growth ( 45 , 46 ). Coadministration of a glutaminase inhibitor with gemcitabine also abrogated MUC5AC (Mucin 5AC)-mediated gemcitabine resistance in mouse and human pancreatic cancers, providing a new target for future immunotherapy ( 47 ).…”

CysModDB: a comprehensive platform with the integration of manually curated resources and analysis tools for cysteine posttranslational modifications

“…In addition, every protein was cross-referenced with three external databases (i.e. Reactome Pathway Database, STRING and dbPTM [ 14 , 22 , 23 ]), providing information about involved pathways, protein–protein interactions and PTM cross-talks.…”

“…As a flood of CysPTM sites were identified, several databases have been developed to host CysPTM information (e.g. RedoxDB [ 13 ], dbPTM [ 14 ], dbSNO [ 15 ], dbGSH [ 16 ], SwissPalm [ 17 ] and iCysMod [ 18 ]). Nevertheless, they have a few limitations.…”

“…These sites consist of 12 different CysPTM types, which is the most extensive compared with previous databases. CysModDB is composed of five parts: (1) PTM site annotations, including flanking regions, sample origin and enrichment techniques, (2) protein annotations, covering sequences with highlighted CysPTM positions, functional regions, subcellular locations and structure information, (3) cross-references to external databases for protein pathways (Reactome [ 22 ]), protein–protein interactions (STRING [ 23 ]) and protein PTMs (dbPTM [ 14 ]), (4) online computational tools for predicting CysPTM sites and 5) an analysis toolkit, composed of gene enrichment analysis, regulatory network and investigation of sequence features. The five parts are integrated using a customized graphic browser and a Basket.…”

Thirty years of molecular dynamics simulations on posttranslational modifications of proteins

“…Databases and informatic methods cataloguing general PTM information, 54–66 as well as resources depicting experimentally-validated or computationally-predicted sites specific for phosphorylation, 67–88 glycosylation, 80,89–98 and acylation, 80,99–119 among other modification forms, 80,120–132 exist. These resources can be used to identify PTM sites on target proteins for improved molecular modeling.…”