Table 2.
PTM resource database
| No. | Short Name | DB Name | URLs |
|---|---|---|---|
| 1 | dbPTM | A database for exploring regulatory networks and functional associations of protein posttranslational modifications | https://awi.cuhk.edu.cn/dbPTM/ |
| 2 | PTMcode v2 | A resource for functional associations of posttranslational modifications within and between proteins | http://ptmcode.embl.de |
| 3 | PTM-SD | A database of structurally resolved and annotated posttranslational modifications in proteins | http://www.dsimb.inserm.fr/dsimb_tools/PTM-SD/ |
| 4 | FAT-PTM | The Functional Analysis Tools for Posttranslational Modifications (FAT-PTM) database: a PTM database for analysis of proteins and metabolic pathways | https://bioinformatics.cse.unr.edu/fat-ptm/ |
| 5 | PTMD | A Database of Human Disease-associated Posttranslational Modifications | http://ptmd.biocuckoo.org |
| 6 | DEPOD | The Human DEPhOsphorylation Database | http://depod.bioss.uni-freiburg.de/ |
| 7 | iPTMnet | An integrated resource for protein post-translational modification network discovery | http://proteininformationresource.org/iPTMnet |
| 8 | PhosPhAt 4.0 | The Arabidopsis Protein Phosphorylation Site Database: an updated arabidopsis database for searching phosphorylation sites and kinase-target interactions | http://phosphat.uni-hohenheim.de |
| 9 | Phospho.ELM | A database of phosphorylation sites | http://phospho.elm.eu.org |
| 10 | PhosphoGrid | A database of experimentally verified in vivo protein phosphorylation sites from the budding yeast saccharomyces cerevisiae | http://www.phosphogrid.org |
| 11 | PhosphoSitePlus | A knowledgebase dedicated to mammalian post-translational modifications (PTMs) | http://www.phosphosite.org |
| 12 | UniCarbKB | A new database features for integrating glycan structure abundance, compositional glycoproteomics data, and disease associations | http://www.unicarbkb.org/ |
| 13 | VPTMdb | A viral posttranslational modification database | http://vptmdb.com:8787/VPTMdb/ |
| 14 | AWESOME | A database of SNPs that affect protein posttranslational modifications | https://github.com/mgramin/awesome-db-tools |
| 15 | PTM-Switchboard | A database of posttranslational modifications of transcription factors, the mediating enzymes and target genes | http://cagr.pcbi.upenn.edu/PTMswitchboard |
| 16 | PTM-Shepherd | Analysis and Summarization of PostTranslational and Chemical Modifications From Open Search Results | https://github.com/Nesvilab/PTM-Shepherd |
| 17 | iProteinDB | An Integrative Database of Drosophila Post-translational Modifications | https://www.flyrnai.org/tools/iproteindb/web/ |
| 18 | PRISMOID | A comprehensive 3D structure database for posttranslational modifications and mutations with functional impact | https://prism.erc.monash.edu/ |
| 19 | dbGSH | A database of S-glutathionylation | http://csb.cse.yzu.edu.tw/dbGSH/ |
| 20 | qPTMplants | An integrative database of quantitative posttranslational modifications in plants | http://qptmplants.omicsbio.info |
| 21 | novPTmenzy | A database for enzymes involved in novel posttranslational modifications | http://www.nii.ac.in/novptmenzy.html |
| 22 | SysPTM 2.0 | An updated systematic resource for posttranslational modification | http://lifecenter.sgst.cn/SysPTM/ |
| 23 | PHOSIDA | A posttranslational modification database | http://www.phosida.com |
| 24 | BioGRID | A comprehensive biomedical resource of curated protein, genetic, and chemical interactions | https://thebiogrid.org |
| 25 | qPhos | A database of protein phosphorylation dynamics in humans | http://qphos.cancerbio.info |
| 26 | EPSD | Eukaryotic Phosphorylation Site Database: a well-annotated data resource of protein phosphorylation sites in eukaryotes | http://epsd.biocuckoo.cn/ |
| 27 | CPLM 4.0 | An updated database with rich annotations for protein lysine modifications | http://cplm.biocuckoo.cn/ |
| 28 | YAAM | Yeast Amino Acid Modifications Database | http://yaam.ifc.unam.mx/ |
| 29 | HPRD | Human Protein Reference Database | http://www.hprd.org/ |
| 30 | Phospho3D 2.0 | An enhanced database of three-dimensional structures of phosphorylation sites | http://www.phospho3d.org/ |
| 31 | LymPHOS 2.0 | An update of a phosphosite database of primary human T cells | http://www.lymphos.org |
| 32 | P3DB 3.0 | From plant phosphorylation sites to protein networks | http://p3db.org |
| 33 | UniPep | A database for human N-linked glycosites: a resource for biomarker discovery | http://www.unipep.org |
| 34 | GlycoFish | A database of zebrafish N-linked glycoproteins identified using SPEG method coupled with LC/MS | http://betenbaugh.jhu.edu/GlycoFish |
| 35 | mUbiSiDa | A comprehensive database for protein ubiquitination sites in mammals | http://reprod.njmu.edu.cn/mUbiSiDa |
| 36 | SwissPalm | A database on protein S-palmitoylation | https://swisspalm.org/ |