Skip Navigation

Nucleic Acids Research 2006 34(Database Issue):D622-D627; doi:10.1093/nar/gkj083
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1483K) Freely available
Right arrow Screen PDF (233K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Lee, T.-Y.
Right arrow Articles by Wang, T.-H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lee, T.-Y.
Right arrow Articles by Wang, T.-H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
H. R. Ansari, D. R. Flower, and G. P. S. Raghava
AntigenDB: an immunoinformatics database of pathogen antigens
Nucleic Acids Res., October 9, 2009; (2009) gkp830v1.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
C. M. Song, S. J. Lim, and J. C. Tong
Recent advances in computer-aided drug design
Brief Bioinform, September 1, 2009; 10(5): 579 - 591.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
H. Li, X. Xing, G. Ding, Q. Li, C. Wang, L. Xie, R. Zeng, and Y. Li
SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications
Mol. Cell. Proteomics, August 1, 2009; 8(8): 1839 - 1849.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C.-H. Chou, W.-C. Chang, C.-M. Chiu, C.-C. Huang, and H.-D. Huang
FMM: a web server for metabolic pathway reconstruction and comparative analysis
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W129 - W134.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Everett, A. Vo, and S. Hannenhalli
PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D66 - D71.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C.-Y. Li, Q.-R. Liu, P.-W. Zhang, X.-M. Li, L. Wei, and G. R. Uhl
OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D251 - D260.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Ding, P. Lorenz, M. Kreutzer, Y. Li, and H.-J. Thiesen
SysZNF: the C2H2 zinc finger gene database
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D267 - D273.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Lopez, A. Valencia, and M. Tress
FireDB--a database of functionally important residues from proteins of known structure
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D219 - D223.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J.-H. Hung, H.-D. Huang, and T.-Y. Lee
ProKware: integrated software for presenting protein structural properties in protein tertiary structures.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W89 - W94.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.