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• dbPTM 1.0

How to Link:

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

 

PTM Resource:

- Swiss-Prot
- Phospho.ELM
- PhosphoSite
- Phosphorylation Site Database
- OGlycBase
- UbiProt

Version: 2.0
(Dec. 1, 2007)

Welcome to dbPTM!

dbPTM was proposed to integrate experimentally verified PTMs from several databases, and to annotate the predicted PTMs on Swiss-Prot proteins. This update extends dbPTM to a knowledgebase comprisingthe modified sites, solvent accessibility of substrate, protein secondary and tertiary structures, protein domains and protein variations.

Literature related to PTM, protein conservations and substrate site specificity are also analyzed. Moreover, various computational tools have been developed for more than ten PTM types, such as phosphorylation, glycosylation, acetylation, methylation, sulfation and sumoylation. This study compiles a PTM benchmark consisting of all available experimental PTM sites for performance evaluation of these computational tools. The interface is also redesigned and enhanced to facilitate access to the resource.

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Citing dbPTM
T.Y. Lee, H.D. Huang*, J.H. Hung, H.Y. Huang, Y.S. Yang and T.H. Wang. (2006) "dbPTM: An information repository of protein post-translational modification" Nucleic Acids Research, Vol. 34, D622-D627. [PubMed]

Highlight of dbPTM

PTM Benchmark A PTM benchmark comprising the experimental sites for each PTM type was built to provide a standard for evaluating the predictive performance of various prediction tools. Figure shows the process for compiling the PTM benchmark, which is based on the previous work of Chen et al.. To eliminate the redundancy, the protein sequences containing the same type of PTM sites were grouped by a threshold of 30% identity using BLASTCLUST. If the identify of two protein sequences is greater than 30%, then the fragment sequences of the substrates were re-aligned with BL2SEQ. If the fragment sequences of two substrates with the same location are identical, then only one of the substrate sequences was included in the benchmark. The benchmark compiled over ten types of PTM, which had been investigated in the identification of substrate sites.

System Architecture

Improvements of dbPTM Update

To enhance the knowledge of protein post-translational modification, dbPTM was extended to a knowledgebase of PTM referable literatures, orthologous conserved regions, substrate specificity, relationship between PTMs and subcellular localization, and PTM benchmarks. The proposed knowledgebase provides effective information relating to each type of PTM, including orthologous conserved regions, relationship between PTMs and subcellular localization, and the substrate specificity such as the frequency of amino acids, the average solvent accessibility and the frequency of secondary structure surrounding the modified site. Moreover, the proposed PTM benchmark can be adopted to compare the predictive performance of various tools involved in the same type of PTM prediction, based on the same testing set.