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Open Access Data Note

A comprehensive resource for integrating and displaying protein post-translational modifications

Tzong-Yi Lee15, Justin Bo-Kai Hsu1, Wen-Chi Chang16, Ting-Yuan Wang1, Po-Chiang Hsu2 and Hsien-Da Huang134*

Author Affiliations

1 Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan

2 Department of Biological Science and Technology, Institute of Biochemical Engineering, National Chiao Tung University, Hsin-Chu 300, Taiwan

3 Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan

4 Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan

5 Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan

6 Institute of Tropical Plant Science, National Cheng Kung University, Tainan 701, Taiwan

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BMC Research Notes 2009, 2:111  doi:10.1186/1756-0500-2-111

Published: 23 June 2009

Abstract

Background

Protein Post-Translational Modification (PTM) plays an essential role in cellular control mechanisms that adjust protein physical and chemical properties, folding, conformation, stability and activity, thus also altering protein function.

Findings

dbPTM (version 1.0), which was developed previously, aimed on a comprehensive collection of protein post-translational modifications. In this update version (dbPTM2.0), we developed a PTM database towards an expert system of protein post-translational modifications. The database comprehensively collects experimental and predictive protein PTM sites. In addition, dbPTM2.0 was extended to a knowledge base comprising the modified sites, solvent accessibility of substrate, protein secondary and tertiary structures, protein domains, protein intrinsic disorder region, and protein variations. Moreover, this work compiles a benchmark to construct evaluation datasets for computational study to identifying PTM sites, such as phosphorylated sites, glycosylated sites, acetylated sites and methylated sites.

Conclusion

The current release not only provides the sequence-based information, but also annotates the structure-based information for protein post-translational modification. The interface is also designed to facilitate the access to the resource. This effective database is now freely accessible at http://dbPTM.mbc.nctu.edu.tw/ webcite.