%0 Journal Article %T A comprehensive resource for integrating and displaying protein post-translational modifications %A Tzong-Yi Lee %A Justin Hsu %A Wen-Chi Chang %A Ting-Yuan Wang %A Po-Chiang Hsu %A Hsien-Da Huang %J BMC Research Notes %D 2009 %I BioMed Central %R 10.1186/1756-0500-2-111 %X 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.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.Protein Post-Translational Modification (PTM) plays a critical role in cellular control mechanism, including phosphorylation for signal transduction, attachment of fatty acids for membrane anchoring and association, glycosylation for changing protein half-life, targeting substrates, and promoting cell-cell and cell-matrix interactions, and acetylation and methylation of histone for gene regulation [1]. Several databases collecting information about protein modifications have been established through high-throughput mass spectrometry in proteomics. UniProtKB/Swiss-Prot [2] collects many protein modification information with annotation and structure. Phospho.ELM [3], PhosphoSite [4] and Phosphorylation Site Database [5] were developed for accumulating experimentally verified phosphorylation sites. PHOSIDA [6] integrates thousands of high-confidence in vivo %U http://www.biomedcentral.com/1756-0500/2/111