Welcome to ViralPhos
ViralPhos is a web server for identifying potential virus phosphorylation sites with substrate motifs.
Phosphorylation of virus proteins is linked to viral replication, which leads to an inhibition of normal host-cell functions. This has motivated the field to further elucidate the process of phosphorylation in viral proteins. However, few studies have investigated substrate motifs in identifying virus phosphorylation sites. Additionally, mass spectrometry-based experiments used to investigate such tend to be time-consuming and labor-intensive.
329 experimentally verified phosphorylation fragments on 111 virus proteins were collected from virPTM. These were clustered into subgroups of significantly conserved motifs using a recursively statistical method. Two-layered Support Vector Machines (SVMs) is then applied to train a predictive model for the identified substrate motifs. The SVM models are evaluated using a five-fold cross validation which yields an average accuracy of 0.86 for serine, and 0.81 for threonine. Furthermore, the proposed method is shown to perform at par with three other phosphorylation site prediction tools: PPSP, KinasePhos 2.0 and GPS 2.1.
In this study, we propose a computational method, ViralPhos, which aims to investigate virus substrate site motifs and identify potential phosphorylation sites on virus proteins. We identified informative substrate motifs that matched with several well-studied kinase groups as potential catalytic kinases for virus protein substrates. The identified substrate motifs were further exploited to identify potential virus phosphorylation sites.