Abstract
BackgroundProkaryotic ubiquitin-like protein (Pup), the firstly identified post-translational protein modifier in prokaryotes, is an important signal for the selective degradation of proteins. Recently, large-scale proteomics technology has been applied to identify a large number of pupylated proteins. The development of a database for managing pupylated proteins and pupylation sites is important for further analyses.DescriptionA database named PupDB is constructed by collecting experimentally identified pupylated proteins and pupylation sites from published studies and integrating the information of pupylated proteins with corresponding structures and functional annotations. PupDB is a web-based database with tools for browses and searches of pupylated proteins and interactive displays of protein structures and pupylation sites.ConclusionsThe structured and searchable database PupDB is expected to provide a useful resource for further analyzing the substrate specificity, identifying pupylated proteins in other organisms and developing computational tools for predicting pupylation sites. PupDB is freely available at http://cwtung.kmu.edu.tw/pupdb.
Highlights
Prokaryotic ubiquitin-like protein (Pup), the firstly identified post-translational protein modifier in prokaryotes, is an important signal for the selective degradation of proteins
The structured and searchable database PupDB is expected to provide a useful resource for further analyzing the substrate specificity, identifying pupylated proteins in other organisms and developing computational tools for predicting pupylation sites
The PupDB database is a comprehensive repository of pupylated proteins and pupylation sites with a webbased user interface
Summary
The PupDB database is a comprehensive repository of pupylated proteins and pupylation sites with a webbased user interface. The built-in tools for browses, searches and interactive displays of protein structures and pupylation sites make PupDB a useful resource for further analyzing the substrate specificity, identifying pupylated proteins in other organisms and developing computational tools for predicting pupylation sites. The exported dataset of pupylated proteins is downloadable at PupDB. A predictor GPS-PUP [24] is available for predicting pupylation sites, PupDB with 215 pupylation sites can be utilized to further improve GPS-PUP trained on only 127 pupylation sites. The development and integration of prediction tools based on the dataset of PupDB would be useful for analyzing and predicting pupylation sites. The Java Runtime Environment (JRE) is required for interactive displays of protein 3D structures by Jmol
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