VPTMdb: a viral posttranslational modification database

In viruses, posttranslational modifications (PTMs) are essential for their life cycle. Recognizing viral PTMs is very important for a better understanding of the mechanism of viral infections and finding potential drug targets. However, few studies have investigated the roles of viral PTM5 in virus-human interactions using comprehensive viral PTM datasets. To fill this gap, we developed the first comprehensive viral posttranslational modification database (VPTMdb) for collecting systematic information of PTM5 in human viruses and infected host cells. The VPTMdb contains 1240 unique viral PTM sites with 8 modification types from 43 viruses (818 experimentally verified PTM sites manually extracted from 150 publications and 422 PTM5 extracted from SwissProt) as well as 13 650 infected cells' PTM5 extracted from seven global proteomics experiments in six human viruses. The investigation of viral PTM sequences motifs showed that most viral PTM5 have the consensus motifs with human proteins in phosphorylation and five cellular kinase families phosphorylate more than 10 viral species. The analysis of protein disordered regions presented that more than 50% glycosylation sites of double-strand DNA viruses are in the disordered regions, whereas single-strand RNA and retroviruses prefer ordered regions. Domain-domain interaction analysis indicating potential roles of viral PTM5 play in infections. The findings should make an important contribution to the field of virus-human interaction. Moreover, we created a novel sequence-based classifier named VPTMpre to help users predict viral protein phosphorylation sites. VPTMdb online web server (http://vptmdb.com:8787/VPTMdbt) was implemented for users to download viral PTM data and predict phosphorylation sites of interest.

Automated summary

Posttranslational modifications (PTMs) play essential roles in the life cycle of viruses, and understanding viral PTMs is crucial for studying viral infections and potential drug targets. The development of the comprehensive viral posttranslational modification database (VPTMdb) provides systematic information on PTM sites in human viruses and infected cells, aiding in the investigation of virus-host interactions. The analysis of viral PTM sequences, protein disordered regions, and domain-domain interactions reveals important insights into the roles of viral PTMs in infections and can contribute significantly to the field of virus-human interactions. Additionally, the creation of the VPTMpre classifier and the implementation of the VPTMdb online web server offer valuable tools for users to predict viral protein phosphorylation sites and access viral PTM data.