Table 1.
PTM prediction webservers. Abbreviations: artificial neuronal network (ANN); support vector machine (SVM); random forest method (RFM); Hidden Markov model (HMM); weight matrix (WM); group based phosphorylation scoring method (GPS); binary profile of patterns (BPP); composition profile of patterns (CPP); PSSM profile of patterns (PPM); average surface accessibility (ASA); neuronal network (NN); knowledge-based (KB); conditional random field (CRF); group-based prediction (GBP); binary profile bayesian (BPB); information gain (IG); Bayesian discriminant (BD); enrichment based method (EBM); binary-relative adaptive binomial score Bayesian (Bi-BSP); logistic regression model (LRM); synthetic minority oversampling technique (SMOT); Markov chain clustering (MCC); particle swarm optimization (PSO); genetic variability (GV); position frequency matrix (PFM); covariance discriminant algorithm (CD): machine learning (ML).
| PTM type | Covalent attachment of small chemical groups Web server and URL |
Year | Description | Method | Information | |
|---|---|---|---|---|---|---|
| Phosphorylation | NetPhos 3.1 | http://www.cbs.dtu.dk/services/NetPhos/ | 1999 | K-specific and K-independent | ANN | Prediction based on 17 different kinases |
| Scansite | http://scansite.mit.edu | 2003 | K-specific | WM | Identification of short protein sequence motifs that are recognized by modular signaling domains or mediated specific interaction with proteins | |
| PhosphoSitePlus | http://www.phosphosite.org/siteSearchAction.action | 2004 | K-specific | – | Repository of human and mouse phosphorylation sites | |
| GPS | http://gps.biocuckoo.org/online.php | 2005 | K-specific | GPS | Prediction based on 71 PK groups (e.g. Aurora-A, Aurora-B and NIMA) | |
| KinasePhos 2.0 | http://kinasephos2.mbc.nctu.edu.tw | 2007 | K-specific | SVM | SVM coupled with protein coupling pattern | |
| PhosphoELM | http://phospho.elm.eu.org | 2010 | K-independent | – | Repository of in vivo and in vitro phosphorylation sites | |
| PPRED | http://biomecis.uta.edu/~ashis/res/ppred/ | 2010 | K-independent | SVM | Prediction based on evolutionary information | |
| PhosPhortholog | http://www.phosphortholog.com | 2015 | K-independent | – | Database for cross-species comparison | |
| Glycosylation | bigPI | http://mendel.imp.ac.at/gpi/gpi_server.html | 1999 | GPI-anchor | KB | Prediction for protozoa and metazoa |
| O-GlycBase | http://www.cbs.dtu.dk/databases/OGLYCBASE/ | 1999 | O-glycosylated | – | Repository of O-glycosylated proteins based on protein sequence database and scientific literature | |
| GlycoMod | http://web.expasy.org/glycomod/ | 2001 | N-,O-glycosylated | Experimental determined | Match between the experimentally determined masses and the predicted protease (SWISSPROT and TrEMBL databases) | |
| YinOYang | http://www.cbs.dtu.dk/services/YinOYang/ | 2001 | N-,C-,O-glycosylated | NN | Prediction based on eukaryotes protein sequences | |
| NetNGlyC | http://www.cbs.dtu.dk/services/NetNGlyc/ | 2002 | N-glycosylated | NN | Prediction for procaryotes | |
| GlyProt | http://www.glycosciences.de/glyprot/ | 2005 | N-glycosylated | SWEET-II | 3D model of glycoproteins based on a PDB structure without attached glycans | |
| GPP | http://comp.chem.nottingham.ac.uk/glyco/ | 2008 | N-,C-,O-glycosylated | RF | Prediction of glycosylation sites and the propensity of association with modified residues | |
| NGlycPred | https://exon.niaid.nih.gov/nglycpred/ | 2012 | N-glycosylated | RF | Combination of different structure and residues pattern information | |
| GLYCOPP | http://www.imtech.res.in/raghava/glycopp/submit.html | 2012 | N-,O-glycosylated | SVM | Prediction based on different approaches (BPP, CPP, PPP, ASA + BPP) | |
| NetOGlyC | http://www.cbs.dtu.dk/services/NetOGlyc/ | 2013 | O-glycosylated | NN | Prediction for prokaryotes | |
| S-nitrosylation | GlycoMine | http://www.structbioinfor.org/Lab/GlycoMine/#webserver | 2015 | N-,C-,O-glycosylated | RF | Determination of the features important for glycosylation site specificity |
| GPS-SNO | http://sno.biocuckoo.org/online.php | 2010 | SNO sites | GBP | Prediction of putative SNO based on a database of 504 experimentally verified SNO | |
| Methylation | iSNO-PseAAC | http://app.aporc.org/iSNO-PseAAC/ | 2013 | SNO sites | CRF | Identification of nitrosylated protein on an independent data set (731 experimentally verified SNO and 810 experimentally non verified SNO) |
| MeMo | http://www.bioinfo.tsinghua.edu.cn/~tigerchen/memo.html | 2006 | R-,L-methylated | SVM | Prediction based on orthogonal binary coding scheme for representing protein sequence fragments | |
| BPB-PPMS | http://www.bioinfo.bio.cuhk.edu.hk/bpbppms/ | 2009 | R-,L-methylated | BPB and SVM | Prediction based on experimental data | |
| MASA | http://masa.mbc.nctu.edu.tw/ | 2009 | K-,R-,E-,N-methylated | SVM | Prediction based on structural information (SASA and secondary structures) | |
| PMes | http://bioinfo.ncu.edu.cn/inquiries_PMeS.aspx | 2012 | R-,K-methylated | SVM | Prediction based on physiochemical properties (VdW volume, position weight aminoacid, composition, solvent, SASA) | |
| MethK | http://csb.cse.yzu.edu.tw/MethK/ | 2014 | K-methylated histone | SVM | Differentiation between K-methylated Histone and K-methylated non-Histone | |
| iMethyl-PseAAC | http://www.jci-bioinfo.cn/iMethyl-PseAAC | 2014 | R-,K-methylated | SVM | Prediction based on physiochemical properties, sequence evolution, biochemical and structural disorder information | |
| N-acetylation | PSSMe | http://bioinfo.ncu.edu.cn/PSSMe.aspx | 2016 | R-,L-methylated | IGF | Prediction based on species-specific models |
| NetAcet | http://www.cbs.dtu.dk/services/NetAcet/ | 2004 | Nα-acetylated | NN | Prediction for yeast and mammalian | |
| PAIL | http://bdmpail.biocuckoo.org/prediction.php | 2006 | Nε-,K-acetylated | BD | Prediction based on dataset of 246 acetylated substrates | |
| N-Ace | http://n-ace.mbc.nctu.edu.tw | 2010 | K-,A-,G-,M-,S- and T-acetylated | SVM | Prediction based on physiochemical properties | |
| ASEB | http://bioinfo.bjmu.edu.cn/huac/ | 2012 | K-acetylated | EBM | Prediction based on protein-protein interaction information | |
| BRABSB-PHKA | http://www.bioinfo.bio.cuhk.edu.hk/bpbphka/ | 2012 | K-acetylated | Bi-BSB | Prediction for human-specific lysine acetylated sites | |
| PSKacePred | http://bioinfo.ncu.edu.cn/inquiries_PSKAcePred.aspx | 2012 | K-acetylated | SVM | Prediction based on amynoacid composition, evolutionary similarity and physiochemical properties | |
| LAceP | http://www.scbit.org/iPTM/ | 2014 | K-acetylated | LRM | Prediction based on physiochemical properties | |
| PTM type | Covalent attachment of acyl chains Web server and URL |
Year | Description | Method | Information | |
|---|---|---|---|---|---|---|
| Palmitoylation | CSS-Palm | http://csspalm.biocuckoo.org/online.php | 2008 | Palmitoylated sites | Clustering and scoring algorithm |
Prediction for budding yeast |
| CKSAAP-Palm | http://doc.aporc.org/wiki/CKSAAP-Palm | 2009 | Palmitoylated sites | SVM | Prediction based on protein sequences | |
| SwissPalm | http://swisspalm.epfl.ch | 2015 | Palmitoylated sites | – | Repository of different palmitoylation-proteomic studies | |
| N-myristoylation | SeqPalm | http://lishuyan.lzu.edu.cn/seqpalm/ | 2015 | Palmitoylated sites | SMOT | Correlation between the disruption of palmitoylation sites and diseases |
| NMT | http://mendel.imp.ac.at/myristate/SUPLpredictor.htm | 2002 | N-myristoylated sites | PSIC algorithm | Identification of the N-myristoylated sites processing terminal glycine or internal glycine | |
| Prenylation | Myristoylator | http://web.expasy.org/myristoylator/ | 2004 | N-myristoylated sites | NN | Supplementary tool for NMT. |
| PrePS | http://mendel.imp.ac.at/sat/PrePS/ | 2005 | Farnesylated and geranygeranylated | MCC | Prediction based on first sequences and physical properties | |
| PTM type | Small proteins Web server and URL |
Year | Description | Method | Information | |
|---|---|---|---|---|---|---|
| Sumoylation | SUMOhydro | http://protein.cau.edu.cn/others/SUMOhydro/ | 2012 | Sumoylated sites | SVM | Prediction based on amino acid hydrophobicity |
| GPS-SUMO | http://sumosp.biocuckoo.org/online.php | 2014 | Sumoylated sites | GPS and PSO | Investigation on the relationship between sumoylation and sumo interaction process | |
| SUMOAMVR | http://bioinfo.ncu.edu.cn/SUMOAMVR_Prediction.aspx | 2014 | Sumoylated sites | GV | Investigation on the impact of sumo sites in human diseases | |
| JASSA | http://www.jassa.fr | 2015 | Sumoylated sites | PFM | Identification of database hits, analysis of physicochemical properties and systematic pattern search | |
| pSumo-CD | http://www.jci-bioinfo.cn/pSumo-CD | 2016 | Sumoylated sites | CD | Prediction based on the integration of sequence-coupled information into general pseudo-aminoacid composition | |
| Ubiquitylation | UbPred | http://www.ubpred.org | 2009 | Ubiquitylated sites | RF | Prediction based on first sequences and structural information |
| UbiProber | http://bioinfo.ncu.edu.cn/ubiprober.aspx | 2013 | Ubiquitylated sites | ML | Prediction of species-specific ubiquitinated sites from experimental data | |
| iUbiq-Lys | http://www.jci-bioinfo.cn/iUbiq-Lys | 2014 | Ubiquitylated sites | RF | Prediction based on evolutionary information | |
| UbiNet | http://140.138.144.145/~ubinet/index.php | 2016 | E3 binding/recognition sites | - | Repository of experimental data, ubiquitylated substrates and protein-protein interactions |