ArticleBMC bioinformatics2023
DePolymerase Predictor (DePP): a machine learning tool for the targeted identification of phage depolymerases.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers, 1 of them a synthesis that pooled it.
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Who cites it
50 citing papers in PubMed, 1 synthesis or guideline pooled it, 58 citations in OpenAlex.
- Precision phage therapy in the AI/ML era: a systematic review of discovery-to-clinical translation evidence.Frontiers in microbiology · 2026Pooled it
- Phage-derived depolymerase targeting the K27 capsule impairsEmerging microbes & infections · 2026Article
- Evaluation of a phage-inclusive multimodal strategy for recurrent urinary tract infections.BMC microbiology · 2026Article
- Characterization and therapeutic potential of DepZ57, a stable depolymerase targeting hypervirulent K57Applied and environmental microbiology · 2026Article
- Phenotypic heterogeneity shapes phage resistance and cocktail efficacy inMicrobiology spectrum · 2026Article
- Isolation and characterization of broad-rangeMicrobiology (Reading, England) · 2026Article
- DposFinder: an interpretable transformer model for predicting phage-derived polysaccharide depolymerases and their host capsular serotypes.Genome medicine · 2026Article
- Genomic and biological characterization of lytic phages infecting Pseudomonas syringae associated with almond bacterial blast.Scientific reports · 2026Article
- Characterization, genomic insights and anti-biofilm potential of phage vB_PaeM_PKMS3, a lytic Pbunavirus capable of infecting clinical Pseudomonas aeruginosa isolates.Antonie van Leeuwenhoek · 2026Article
- From structure to design: experimental and AI-driven approaches in receptor-binding protein engineering for reprogramming phage host range.Archives of microbiology · 2026Review
- Genome characterization and receptor-binding protein identification of Klebsiella phage vB_VIPKPNMC05, a member of a novel viral family Pituviridae.Archives of virology · 2026Article
- Efficacy of a novel bacteriophage in controlling Escherichia coli associated with swine farm environments and its potential for biofilm disruption.Scientific reports · 2026Article
- Identification and characterization of Phi1 and Phi3 bacteriophages targeting Xylella fastidiosa subsp. pauca, the causal agent of olive quick decline in Italy.Scientific reports · 2026Article
- Mining a vibriophage depolymerase for enhanced pathogen control in aquaculture.Applied and environmental microbiology · 2026Article
- Stable co-existence ofmBio · 2026Article
- Genomic and Functional Characterization of LyticBiology · 2026Article
- Phage Therapy in Plant Disease Management: 110 Years of History, Current Challenges, and Future Trends.Plants (Basel, Switzerland) · 2026Review
- Bacteriophage Therapy AgainstMicroorganisms · 2026Review
- The Role of Genomics in Advancing and Standardising Bacteriophage Therapy.Antibiotics (Basel, Switzerland) · 2026Review
- Genome-guided isolation and characterization of a novel bacteriophage infectingFrontiers in microbiology · 2026Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biofilm production plays a clinically significant role in the pathogenicity of many bacteria, limiting our ability to apply antimicrobial agents and contributing in particular to the pathogenesis of chronic infections. Bacteriophage depolymerases, leveraged by these viruses to circumvent biofilm mediated resistance, represent a potentially powerful weapon in the fight against antibiotic resistant bacteria. Such enzymes are able to degrade the extracellular matrix that is integral to the formation of all biofilms and as such would allow complementary therapies or disinfection procedures to be successfully applied. In this manuscript, we describe the development and application of a machine learning based approach towards the identification of phage depolymerases. We demonstrate that on the basis of a relatively limited number of experimentally proven enzymes and using an amino acid derived feature vector that the development of a powerful model with an accuracy on the order of 90% is possible, showing the value of such approaches in protein functional annotation and the discovery of novel therapeutic agents.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.