VPTMdb

VPTMdb curates and organizes viral posttranslational modification (PTM) data to support analysis of virus–host interactions and identification of PTM-related therapeutic targets.

Key Features:

• Extensive Data Collection: Contains 1,240 unique viral PTM sites across eight modification types from 43 viruses, including 818 experimentally verified sites manually curated from 150 publications and 422 PTMs extracted from SwissProt.
• Host Cell Interaction Data: Includes 13,650 PTMs identified in host cells infected by six human viruses derived from seven global proteomics experiments.
• Motif and Sequence Analysis: Provides viral PTM sequence motif analyses showing many viral PTMs share consensus motifs with human proteins, with phosphorylation involving more than ten viral species and five cellular kinase families.
• Structural Insights: Reports structural analyses indicating that over 50% of glycosylation sites in double-strand DNA viruses lie within disordered regions, while single-strand RNA and retroviruses preferentially locate glycosylation sites in ordered regions.
• Domain–Domain Interaction Analysis: Contains domain–domain interaction studies that suggest potential roles of viral PTMs in the infection process.
• Predictive Tool - VPTMpre: Integrates VPTMpre, a sequence-based classifier for predicting phosphorylation sites on viral proteins.

Scientific Applications:

• Virus–Human Interaction Studies: Enables investigation of molecular mechanisms of virus–host interactions via comprehensive viral and host PTM data.
• Drug Target Identification: Supports identification of PTM-related therapeutic targets by detailing how viral proteins are modified and interact with host machinery.
• Proteomics Research: Provides reference PTM datasets for comparison and validation of proteomics studies on viral infections.

Methodology:

Manual curation from 150 publications and integration of SwissProt entries and seven global proteomics experiments, combined with motif analysis, structural (disorder) predictions, domain–domain interaction analysis, and a sequence-based classifier (VPTMpre) for phosphorylation-site prediction.