PDP-Miner

PDP-Miner detects prophage tail proteins with depolymerase domains across bacterial genomes, aiding in the identification of potential antibiotic alternatives.

Key Features:

• Ab initio phage tail protein annotation: Annotates phage tail proteins de novo from bacterial genome data.
• Depolymerase activity detection: Detects depolymerase activity within candidate phage tail proteins using an existing machine learning-based prediction tool (Depolymerase-Predictor).
• Post-hoc domain annotation: Performs post-hoc validation by annotating protein domains to investigate for domains indicative of depolymerase activity.

Scientific Applications:

• Antibiotic alternative discovery: Identifies phage depolymerase gene candidates as potential alternatives to conventional antibiotics against antibiotic-resistant bacteria.
• Large-scale bacterial genome screening: Enables detection of depolymerase candidates across thousands of bacterial genomes, as demonstrated with 1,294 Pseudomonas genomes from the International Pseudomonas Consortium Database.

Methodology:

PDP-Miner wraps an existing machine learning-based phage depolymerase prediction tool (Depolymerase-Predictor) to annotate phage tail proteins ab initio, detect depolymerase activity within candidate proteins, and perform post-hoc domain annotation for validation.