PupDB is a database of pupylated proteins and pupylation sites aiming to provide an easily accessible web service for the analysis of pupylated proteins. Hyperlinks to major protein, structure and annotation databases are provided for accessing related information. Four useful tools are constructed and integrated into PupDB to provide functions of browses, keyword searches, sequence similarity searches and interactive displays of protein structures.
For each protein, the corresponding information consists of six major parts of basic information (a), PDB ID (b), gene ontology (GO) annotation (c), pupylation site (d), protein sequence (e) and structure (f).
Further GO information can be accessed by clicking the hyperlink of 'Detailed GO annotation' that links to the corresponding entry of QuickGO.
Users can browse all data collected in PupDB by selecting the 'Browse' option. All proteins will be shown in a sortable table. The entry with 'Y' in the field of 'Site' is a pupylated protein. Otherwise, it is a candidate pupylated protein with 'N' in the field of 'Site'. By clicking the caption of a specific column in a sortable table, the output table will be sorted according to data of the selected column. Furthermore, users can specify the number of rows shown per page.
The tool of keyword search can be accessed by selecting the 'Search' option. There are five fields for searching PupDB including description, UniProt AC, gene name, organism and protein type. By entering keywords for any one or combination of the fields, PupDB will return search results as a sortable table according to the user input keywords.
Users can enter a protein sequence of interest in FASTA format to perform a BLAST  search against PupDB to fetch entries with a user-defined threshold of E-value. The BLAST tool can serve as a potentially useful tool for predicting promising pupylation sites by sequence similarity. In addition to the protein information, two additional columns of scores and E-values obtained from the BLAST search are included in the output sortable table. The detailed information of BLAST sequence alignment can be downloaded by clicking the download link.
The exported tab-delimited table is available at http://cwtung.kmu.edu.tw/pupdb/pupdb_export.tab
If you find PupDB useful. Please cite:
Tung, C.-W. (2012) PupDB: a database of pupylated proteins, BMC Bioinformatics, 13, 40.