Welcome to dbPTM 10th Year Anniversary

dbPTM is an integrated resource for protein post-translational modifications (PTMs). Due to the importance of protein post-translational modifications (PTMs) in regulating biological processes, the dbPTM was developed as a comprehensive database by integrating experimentally verified PTMs from several databases and annotating the potential PTMs for all UniProtKB protein entries.

In this 10th year anniversary, dbPTM aims to be an integrated resource not only accumulating comprehensive dataset of experimentally verified PTMs supported with literatures but also providing an integrative interface for accessing all available databases and tools associated with PTM analyses.

   

In addition to collecting experimental PTM data from 14 public databases, this update manually curates more than 12,000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles which were retrieved by a text mining approach. With an increasing number of various PTM prediction methods, this work compiles non-homologous benchmark datasets to evaluate the predictive power among online PTM prediction tools in order to provide suggestions to users with the need to predict PTM sites with high sensitivity (Sn), high specificity (Sp), or balanced Sn and Sp.

An increasing interest in structural investigation of PTM substrate sites motivated us to map all experimental PTM peptides to PDB protein entries by sequence identity, which enables users to study spatial amino acid composition, solvent-accessible surface area, and spatially neighboring amino acids for PTM substrate sites based on tertiary structures. In particular, the side chain orientations of the amino acids spatially surrounding the PTM substrate sites were determined for exploring the functional roles and drug-binding effects of the spatially neighboring amino acids to the substrate sites. Due to the annotation of drug binding in PDB, this update has identified over 1,100 PTM sites which are associated with the drug binding. Furthermore, this update has integrated the information of metabolic pathways and protein-protein interactions (PPIs) to implement the network analysis for a group of genes/proteins.

Integrative Platform for PTM Analysis

Databases

[Jump to Tools]

Glycosylation | Phosphorylation | Acetylation | Methylation | S-nitrosylation | Ubiquitination | Myristoylation | Prenylation | S-glutathionylation | Multiple

Glycosylation

GlycoEpitopeGlycoEpitope: A Database of Carbohydrate Epitopes and Antibodies
GlycoFishGlycoFish: a database of zebrafish N-linked glycoproteins identified using SPEG method coupled with LC/MS.21591763
GlycoFlyGlycoFly: a database of Drosophila N-linked glycoproteins identified using SPEG--MS techniques.21480662
GlycomeDBGlycomeDB--a unified database for carbohydrate structures.21045056
GlycoProtDBLarge-scale identification of N-glycosylated proteins of mouse tissues and construction of a glycoprotein database, GlycoProtDB.22823882
UnicarbKBUniCarbkb: building a knowledge platform for glycoproteomics 24234447
GLYCOSCIENCES.deGLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research.16239495
GlycoSuiteDBGlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 12520065
CFGGlycan array data management at?Consortium?for?Functional?Glycomics.25753711
ProGlycProtProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins.22039152
UniPepUniPep--a database for human N-linked glycosites: a resource for biomarker discovery.16901351
dbOGAPdbOGAP - an integrated bioinformatics resource for protein O-GlcNAcylation.21466708
O-GlycBaseO-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.9847232

Phosphorylation

dbPPTdbPPT: a comprehensive database of protein phosphorylation in plants.25534750
dbPSPdbPSP: a curated database for protein phosphorylation sites in prokaryotes.25841437
HPRDHuman Protein Reference Database--2009 update.18988627
LymPHOSLymPHOS: design of a phosphosite database of primary human T cells.19639593
MAPResExploring the sequence context of phosphorylatable amino acids: the contribution of the upgraded MAPRes tool.25258092
P3DBP3DB: a plant protein phosphorylation database.18931372
PepCyber:P~PEPPepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains.18160410
PHOSIDAPHOSIDA 2011: the posttranslational modification database.21081558
PhosPhAtPhosPhAt goes kinases--searchable protein kinase target information in the plant phosphorylation site database PhosPhAt23172287
Phospho.ELMPhospho.ELM: a database of phosphorylation sites--update 201121062810
Phospho3DPhospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites20965970
PhosphoGRIDThe PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update23674503
PhosphoNETPrediction of 492 human protein kinase substrate specificities22165948
PhosphoPOINTPhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database.18689816
PhospoPepPhosphoproteome resource for systems biology research21082442
PhosSNPPhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation19995808
SubPhosProteomic analysis and prediction of human phosphorylation sites in subcellular level reveal subcellular specificity25236462

Acetylation

CPLACPLA 1.0: an integrated database of protein lysine acetylation21059677

Methylation

PubMethPubMeth: a cancer methylation database combining text-mining and expert annotation.17932060

S-nitrosylation

dbSNOdbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation.25399423

Ubiquitination

UbiProtUbiProt: a database of ubiquitylated proteins.17442109

Myristoylation

MYRbaseMYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins. Genome biology.15003124

Prenylation

PRENbaseTowards complete sets of farnesylated and geranylgeranylated proteins.17411337

S-glutathionylation

dbGSHdbGSH: a database of S-glutathionylation.24790154

Multiple PTMs

CPLMCPLM: a database of protein lysine modifications.24214993
CrosstalkDBLarge scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk24741113
HIstomeHIstome--a relational knowledgebase of human histone proteins and histone modifying enzymes.22140112
novPTMenzynovPTMenzy: a database for enzymes involved in novel post-translational modifications.25931459
ProteomeScoutProteomeScout: a repository and analysis resource for post-translational modifications and proteins.25414335
PSPPhosphoSitePlus, 2014: mutations, PTMs and recalibrations.25514926
PTMCodePTMcode v2: a resource for functional associations of post-translational modifications within and between proteins25361965
PTMfuncSystematic functional prioritization of protein posttranslational modifications.22817900
PTM-SDPTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins.24857970
RedoxDBRedoxDB--a curated database for experimentally verified protein oxidative modification.22833525
RESIDThe RESID Database of Protein Modifications: 2003 developments.12520062
SysPTMSysPTM 2.0: an updated systematic resource for post-translational modification.24705204
topPTMtopPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins.24302577

Tools

[Jump to Databases]

Glycosylation | Phosphorylation | Acetylation | Methylation | S-nitrosylation | Ubiquitination | GPI-lipid anchor modified |
Myristoylation | Prenylation | Pupylation | S-glutathionylation | Succinylation | SUMOylation | Sulfation | Multiple

Glycosylation

EnsembleGlyGlycosylation site prediction using ensembles of Support Vector Machine classifiers.17996106
GlycoMineGlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome.25568279
GlycoPPGlycoPP: a webserver for prediction of N- and O-glycosites in prokaryotic protein sequences.22808107
GPPPrediction of glycosylation sites using random forests.19038042
GS-alignGS-align for glycan structure alignment and similarity measurement.25857669
GlycoEPIn silico Platform for Prediction of N-, O- and C-Glycosites in Eukaryotic Protein Sequences23840574
NetNGlycNetNGlyc: Prediction of N-glycosylation sites in human proteins
GECSPrediction of glycan structures from gene expression data based on glycosyltransferase reactions16159923
YinOYangPrediction of glycosylation across the human proteome and the correlation to protein function.11928486
DictyOGlycScanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks.10521537
NetOGlycPrecision mapping of the human O-GalNAc glycoproteome through SimpleCell technology.23584533
OglycPredicting? O-glycosylation sites in mammalian proteins by using SVMs16731044

Phosphorylation

AMSAMS 4.0: consensus prediction of post-translational modifications in protein sequences.22555647
CKSAAP_PhSitePrediction of protein phosphorylation sites by using the composition of k-spaced amino acid pairs.23110047
CRPhosPrediction of kinase-specific phosphorylation sites using conditional random fields.18940828
DAPPLEAPPLE: a pipeline for the homology-based prediction of phosphorylation sites.23658419
DISPHOSThe importance of intrinsic disorder for protein phosphorylation.14960716
GPSGPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection.21062758
HMMpTMHMMpTM: improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction.24225132
KinasePhosKinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns.17517770
KinomeXplorerKinomeXplorer: an integrated platform for kinome biology studies.24874572
MetaPredPSMeta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection.1823471
MusiteMusite, a tool for global prediction of general and kinase-specific phosphorylation sites.20702892
NetPhorestLinear motif atlas for phosphorylation-dependent signaling.18765831
NetPhosSequence and structure-based prediction of eukaryotic protein phosphorylation sites.10600390
NetPhosKPrediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence.15174133
NetPhosYeastNetPhosYeast: prediction of protein phosphorylation sites in yeast.17282998
phos_predPrediction of protein kinase-specific phosphorylation sites in hierarchical structure using functional information and random forest24452754
Phos3DDetection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins.19383128
PhoScanPrediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach.17680694
PHOSFERComputational phosphorylation site prediction in plants using random forests and organism-specific instance weights.23341503
PHOSITEHighly specific prediction of phosphorylation sites in proteins15297298
PhosphoPICKPhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events25304781
PhosphoRicePhosphoRice: a meta-predictor of rice-specific phosphorylation sites22305189
PhosphoSVMPhosphoSVM: prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine24623121
pkaPSpkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model17222345
PKISPKIS: computational identification of protein kinases for experimentally discovered protein phosphorylation sites23941207
PlantPhosPlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity21703007
PostModPostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship20122181
PPREDMachine learning approach to predict protein phosphorylation sites by incorporating evolutionary information20492656
PPSPPPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory16549034
PredikinThe Predikin webserver: improved prediction of protein kinase peptide specificity using structural information18477637
PredPhosphoPrediction of phosphorylation sites using SVMs15231530
PSEAPSEA: Kinase-specific prediction and analysis of human phosphorylation substrates24681538
PTMPredPrediction of posttranslational modification sites from amino acid sequences with kernel methods24291233
RLIMS-PRLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information25122463
ViralPhosViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins24564381

Acetylation

NetAcetNetAcet: prediction of N-terminal acetylation sites.15539450
N-AceN-Ace: using solvent accessibility and physicochemical properties to identify protein N-acetylation sites.20839302
LysAcetImproved Prediction of Lysine Acetylation by Support Vector Machines 19689425
ASEBASEB: a web server for KAT-specific acetylation site prediction22600735
BRABSB-PHKASystematic analysis of human lysine acetylation proteins and accurate prediction of human lysine acetylation through bi-relative adapted binomial score Bayes feature representation22936054
PAILPrediction of N?-acetylation on internal lysines implemented in Bayesian Discriminant Method17045240
LAcePLAceP: Lysine Acetylation Site Prediction Using Logistic Regression Classifiers24586884
PSKAcePredPosition-specific analysis and prediction for protein lysine acetylation based on multiple features.23173045

Methylation

BPB-PPMSComputational Identification of Protein Methylation Sites through Bi-Profile Bayes Feature Extraction 19290060
iMethyl-PseAACiMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach24977164
MASAIncorporating?structural?characteristics?for?identification?of?protein?methylation?sites.19263424
MeMoMeMo: a web tool for prediction of protein methylation modifications.16845004

S-nitrosylation

GPS-SNOGPS-SNO: computational prediction of protein S-nitrosylation sites with a modified GPS algorithm.20585580
iSNO-AAPairiSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins.24109555
iSNO-PseAACiSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition.23409062
PSNOPSNO: predicting cysteine S-nitrosylation sites by incorporating various sequence-derived features into the general form of Chou's PseAAC.24968264

Ubiquitination

hCKSAAP_UbSitehCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.23603789
iUbiq-LysiUbiq-Lys: prediction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a gray system model.25248923
UbiPredComputational identification of ubiquitylation sites from protein sequences.18625080
UbiProberIncorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites.23626001
UbPredIdentification, analysis, and prediction of protein ubiquitination sites.19722269

GPI-lipid anchor modified

big-Pi plantGlycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for Arabidopsis and rice14681532
FragAnchorFragAnchor: a large-scale predictor of glycosylphosphatidylinositol anchors in eukaryote protein sequences by qualitative scoring17893077
GPI-SOMIdentification of GPI anchor attachment signals by a Kohonen self-organizing map15691858
PredGPIPredGPI: a GPI-anchor predictor18811934

Myristoylation

NMTPrediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1.12824382

Prenylation

PrePSRefinement and prediction of protein prenylation motifs.15960807

Pupylation

GPS-PUPGPS-PUP: computational prediction of pupylation sites in prokaryotic proteins.21850344

S-glutathionylation

GSTPredSupport vector machine based prediction of glutathione S-transferase proteins.17627599

Succinylation

iSuc-PseAACiSuc-PseAAC: predicting lysine succinylation in proteins by incorporating peptide position-specific propensity26084794

SUMOylation

GPS-SUMOGPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs24880689
JASSAJASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs26142185
SUMOhydroSUMOhydro: a novel method for the prediction of sumoylation sites based on hydrophobic properties22720073
SUMOplot

Multiple PTMs

CarSPredCarSPred: a computational tool for predicting carbonylation sites of human proteins.25347395
ISSPredISSPred: Identification of Intein proteins and their Splice Sites
ModPredThe structural and functional signatures of proteins that undergo multiple events of post-translational modification24888500
Motifs treeMotifs tree: a new method for predicting post-translational modifications.24681905
NetChopPrediction of proteasome cleavage motifs by neural networks.11983929
NetCoronaCoronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology.15180906
NetPicoRNACleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks.8931139
PAProCPAProC: a prediction algorithm for proteasomal cleavages available on the WWW.11345595
PcleavagePcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences.15988831
PEIMANPEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis25911152
PeptideMap
PHOXTRACKPHOXTRACK-a tool for interpreting comprehensive datasets of post-translational modifications of proteins.25152232
ProPPrediction of proprotein convertase cleavage sites.14985543
PTM-XSystematic characterization and prediction of post-translational modification cross-talk25605461
PyTMsPyTMs: a useful PyMOL plugin for modeling common post-translational modifications.25431162