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Nucleic Acids Research 2006 34(Database Issue):D622-D627; doi:10.1093/nar/gkj083
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Nucleic Acids Research, 2006, Vol. 34, Database issue D622-D627
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

dbPTM: an information repository of protein post-translational modification

Tzong-Yi Lee1, Hsien-Da Huang1,2,*, Jui-Hung Hung1, Hsi-Yuan Huang1, Yuh-Shyong Yang2,3 and Tzu-Hao Wang4

1Institute of Bioinformatics, National Chiao Tung University Hsin-Chu 300, Taiwan 2Department of Biological Science and Technology, National Chiao Tung University Hsin-Chu 300, Taiwan 3Institute of Biochemical Engineering, National Chiao Tung University Hsin-Chu 300, Taiwan 4Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Lin-Kou Medical Center Tao-Yuan 333, Taiwan

*To whom correspondence should be addressed. Tel: +886 3 5712121, ext. 56952; Email: bryan{at}mail.nctu.edu.tw

Received August 15, 2005. Revised October 11, 2005. Accepted October 11, 2005.

dbPTM is a database that compiles information on protein post-translational modifications (PTMs), such as the catalytic sites, solvent accessibility of amino acid residues, protein secondary and tertiary structures, protein domains and protein variations. The database includes all of the experimentally validated PTM sites from Swiss-Prot, PhosphoELM and O-GLYCBASE. Only a small fraction of Swiss-Prot proteins are annotated with experimentally verified PTM. Although the Swiss-Prot provides rich information about the PTM, other structural properties and functional information of proteins are also essential for elucidating protein mechanisms. The dbPTM systematically identifies three major types of protein PTM (phosphorylation, glycosylation and sulfation) sites against Swiss-Prot proteins by refining our previously developed prediction tool, KinasePhos (http://kinasephos.mbc.nctu.edu.tw/). Solvent accessibility and secondary structure of residues are also computationally predicted and are mapped to the PTM sites. The resource is now freely available at http://dbPTM.mbc.nctu.edu.tw/.

Correspondence may also be addressed to Tzu-Hao Wang. Tel: +886 3 3281200, ext. 8984; Email: knoxtn{at}cgmh.org.tw

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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