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Latest news:

June 15th, 2012:
The Pupylated proteins with pupylation sites of PupDB has been integrated into dbPTM!

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How to Link:

Users can directly link to dbPTM by Swiss-Prot ID.
For example:

http://dbPTM.mbc.
nctu.edu.tw/search
_result.php?swiss_id
=H31_HUMAN

 

PTM Resource:

- Swiss-Prot
- Phospho.ELM
- PhosphoSitePlus
- Phosphorylation Site Database
- OGlycBase
- UbiProt
- RegPhos
- PupDB



Version: 3.0
(June 15th, 2012)


dbPTM is an informative resource for protein post-translational modifications (PTMs). Due to the high-throughput of mass spectrometry-based methods in identifying site-specific PTMs, this update integrates experimental PTMs obtained from eleven public resources as well as manually curated MS/MS peptides associated with PTMs from research articles.

In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, over 60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function.

Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and transmembrane topologies. To facilitate the investigation of PTMs on transmembrane proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Lastly, this version features an improved web interface to facilitate convenient access to the resource.

PTM Type
Number of experimental sites
Number of putative sites from Swiss-Prot
Number of putative sites by HMMs
Phosphorylation
153,113
74,365
1,763,427
Ubiquitylation
23,673
2,026
8,865
Acetylation
10,385
19,982
1,195
N-linked Glycosylation
15,678
87,529
471,288
O-linked Glycosylation
3,711
1,834
384,897
Total
221,020
226,122
2,904,184


Citing dbPTM

C.T. Lu, K.Y Huang, M.G. Su, T.Y. Lee, N.A. Bretana, W.C. Chang, Y.J. Chen, Y.J. Chen and H.D. Huang. (2013) "DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications." Nucleic Acids Research, Vol. 41, D295-305. [PubMed]

Highlight of dbPTM 3.0


Improvements of dbPTM 3.0


Due to the high-throughput of mass spectrometry-based proteomics, this update version (dbPTM 3.0) not only integrates experimental PTMs from public resources but also manually curates MS/MS peptides associated with PTMs from research articles. The dbPTM 3.0 aims to be an informative resource for investigating the substrate site specificity and functional association of PTMs. The highlighted improvements in dbPTM 3.0 are illustrated as follows:
1. This update manually curates more than 3000 PTM peptides from approximately 250 research articles using text mining approach, especially for the emerging PTM, cysteine S-Nitrosylation.
2. In order to investigate the substrate specificity for modification sites, MDDLogo (Lee et al., 2011) has been applied to identify the significant substrate motifs for each type of PTMs containing more than 50 modified peptides.
3. Many PTMs can create binding sites for specific protein-interaction domains (Seet et al., 2006). These domains work together for cellular function and read the state of proteome to cellular organization. Thus, this update integrates the information of protein-protein interactions and domain-domain interactions to determine the functional association for the PTM site which locates in functional domain.
4. With the importance of PTMs functioning on transmembrane proteins, the information of membrane topologies is collected from TMPad, TOPDb, PDBTM, and OPM. The structural topology of transmembrane proteins is represented by graphical visualization, as well as the PTMs. Moreover, the tertiary structure of PTM sites on transmembrane proteins is visualized by Jmol program.
5. Web interface is also redesigned and enhanced to facilitate access to the resource.