 |
PTM prediction tools
This is a survey of publicly available PTM web resources, databases and classification/prediction servers.
Resource | Classification | Reference | Information/ |
| method/Database | | PMID |
| | | |
General PTM-related | | | |
| | | |
ELM | Consensus | 1 | Predicts Eukaryotic Linear Motifs (ELMs) based on |
| patterns | | consensus patterns. Applies context-based rules |
| | | and logical filters. PMID:12824381 |
PROSITE | Consensus | 2 | Curated database of consensus patterns for many |
| patterns | | types of PTMs, including phosphorylation sites. |
| | | MotifScan feature allows for scanning of query |
| | | sequence. PMID:12230035 |
HPRD | Database | 3 | Human Protein Reference Database (HPRD). |
| | | Highly curated database of disease-related |
| | | proteins and their PTMs. PMID:14681466 |
RESID | Database | 4 | Part of the PIR protein database. Comprehensive |
| | | collection of annotations and structures for PTMs. |
| | | PMID:12520062 |
| | | |
Phosphorylation | | | |
| | | |
Scansite | Weight matrix | 5 | Based on peptide library studies. Predicts kinase- |
| | | specific motifs and other types of motifs involved |
| | | in signal transduction, e.g. SH2 domain binding. |
| | | PMID:11283593 |
PREDIKIN | Expert system | 6 | The program produces a prediction of substrates |
| | | for S/T protein kinases based on the primary |
| | | sequence of a protein kinase catalytic domain. |
| | | PMID:12502784 |
NetPhos | Neural network | 7 | Predicts general phosphorylation status based on |
| | | sets of experimentally validated S, T and Y |
| | | phosphorylation sites. PMID:10600390 |
NetPhosK | Neural network | 8 | Predicts kinase-specific phosphorylation sites |
| | | based on sets of experimentally validated S, T |
| | | and Y phosphorylation sites. PMID:15174133 |
PhosphoELM | Database | 9 | Curated database of validated phosphorylation |
| | | sites. PMID:9847189 |
Phosphosite | Database | | Curated database of in vivo validated phospho- |
| | | rylation sites. |
| | | |
Glycosylation | | | |
| | | |
bigPI | Weight matrix | 10 | Predicts GPI-modification sites using a composite |
| | | prediction function including a weight matrix |
| | | and physical model. PMID:10497036 |
DGPI | Weight matrix | | Predics GPI cleavage site (GPI-anchor) |
| | | in a protein. |
GlycoMod | Look-up table | 11 | Predicts glycan structure from its experimentally |
| | | determined mass. PMID:11680880 |
NetOGlyc | Neural network | 12 | Predicts mucin type CalNac O-glycosylation sites |
| | | in mammalian proteins. PMID:15385431 |
NetNGlyc
| Neural network | 13 | Predicts N-glycosylation sites in human proteins |
| | | by examining the sequence context of Asn- |
| | | Xaa-Ser/Thr sequons. In preparation. |
DictyOGlyc | Neural network | 14 | Predicts GlcNAc o-glycosylation sites in Dictyoste- |
| | | lium discoideum proteins. PMID:10521537 |
YinOYang | Neural network | | Predicts O-beta-GlcNAc attachment sites in eukaryotic |
| | | protein sequences. |
O-GlycBase | Database | 15 | Predicts O-beta-GlcNAc attachment sites in eukaryotic |
| | | protein sequences. PMID:9847232 |
| | | |
Sulfation | | | |
| | | |
Sulfinator | HMM | 16 | Predicts tyrosine sulfation sites using a combination |
| | | of HMM models. PMID:12050077 |
| | | |
Cleavage | | | |
| | | |
ProP | Neural network | 17 | Predicts arginine and lysine propeptide cleavage sites |
| | | in protein sequences. PMID:14985543 |
NetPicoRNA | Neural network | 18 | Predicts picornaviral protease cleavage sites in |
| | | protein sequences. PMID:8931139 |
NetCorona | Neural network | 19 | Predicts coronavirus 3C-like proteinase (or protease) |
| | | cleavage sites on protein sequences. PMID:15180906 |
| | | |
Myristoylation | | | |
| | | |
Myristoylator | Neural network | 20 | Predicts N-terminal myristoylation on protein sequences. |
| | | PMID:15174132 |
NMT | Weight matrix | 21 | Predicts myristoylation sites on protein sequences. |
| | | PMID:11955008 |
| | | |
| | | |
Sumoylation | | | |
| | | |
SUMOplot | Weight matrix | | Prediction of sumoylation on protein sequences. |
| | | |
| | | |
Part of the table has been taken from the review:
"Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence"
Blom, N., Sicheritz-Pontén, T., Gupta, R., Gammeltoft, S. and Brunak, S.
Proteomics 2004, 4, 1633-1649. PMID:15174133
References
1. Puntervoll, P., Linding, R., Gemund, C., Chabanis-Davidson, S. et al., Nucleic Acids Res. 2003, 31, 3625-3630.
2. Sigrist, C., Cerutti, L., Hulo, N., Gattiker, A. et al., Brief Bioinform. 2002, 3, 265-274.
3. Peri, S., Navarro, J., Amanchy, R., Kristiansen, T. et al., Genome Res. 2003, 13, 2363-2371.
4. Garavelli, J., Nucleic Acids Res. 2003, 31, 499-501.
5. Yaffe, M., Leparc, G., Lai, J., Obata, T. et al., Nat. Biotechnol.2001, 19, 348-353.
6. Brinkworth, R., Breini, R., Kobe, B., Proc. Natl. Acad. USA 2003, 100, 74-79.
7. Blom, N., Gammeltoft, S., Brunak, S., J. Mol. Biol. 1999, 294, 1351-1362.
8. Blom, N., Sicheritz-Pontén, T., Gupta, R.,Gammeltoft, S. et al., Proteomics 2004, 4, 1633-1649.
9. Kreegipuu, A., Blom, N., Brunak, S., Nucleic Acids Res.1999, 27, 237-239.
10. Eisenhaber, B., Bork, P., Eisenhaber, F., J. Mol. Biol. 1999, 292, 741-758.
11. Cooper, C., Gasteiger, E., Packer, N., Proteomics 2001, 1, 340-349.
12. Julenius, K., Mølgaard, A., Gupta, R., Brunak, S., Glycobiology 2005, 15, 153-164.
13. Gupta, R., Jung, E., Brunak, S., In preparation, 2004.
14. Gupta, R., Jung, E., Gooley, A., Williams, K. et al., Glycobiology 1999, 9, 1009-1022.
15. Gupta, R., Birch, H., Rapacki, K., Brunak, S., Hansen, J., Nucleic Acids Res. 1999, 27, 365-370.
16. Monigatti, F., Gasteiger, E., Bairoch, A., Jung, E., Bioinformatics 2002, 18, 769-770.
17. Duckert, P., Brunak, S., Blom, N., Protein Eng. 2004, 17, 107-112.
18. Blom, N., Hansen, J., Blaas, D., Brunak, S., Protein Science, 1996, 5, 2203-2216.
19. Kiemer, L., Lund, O., Brunak, S., Blom, N., BMC Bioinformatics, 2004, 5, 72.
20. Bologna, G., Yvon, S., Veuthey, A.L., Proteomics, 2004, 4, 1626-1632.
21. Maurer-Stroh, S., Eisenhaber, B., Eisenhaber, F., J Mol Biol, 2002, 317, 541-557.
This page is part of the BioSapiens Network funded by the European Commission within its FP6 programme, under the thematic area "Life science, genomics and biotechnology for health", contract number LHSG-CT-2003-503265.
CORRESPONDENCE
Zenia
M. Larsen,
|
This file was last modified Tuesday 4th 2013f June 2013 11:49:21 GMT |
|