Bioinformatics analysis and collection of protein post-translational modification sites in human viruses

Abstract

Motivation:In viruses, post-translational modifications (PTMs) are essential for their life cycle. Recognizing viral PTMs is very important for better understanding the mechanism of viral infections and finding potential drug targets. However, a database of comprehensive PTM information on viruses is not available. Results: To fill this gap, we developed a viral post-translational modification database (VPTMdb) for collecting systematic information of viral PTM data. The VPTMdb contains 912 PTM sites that integrate 414 experimental-confirmed PTM sites with 98 proteins in 45 human viruses manually extracted from 162 publications and 498 PTMs extracted from UniProtKB/Swiss-Prot. Moreover, we created a novel sequence-based classifier named VPTMpre to help users predict viral protein phosphorylated sites. Finally, an online web server was implemented for users to download viral PTM data and predict phosphorylated sites of interest. Availability and Implementation: VPTMdb can be accessed at