ArticlePLoS computational biology2024
DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 2 of them syntheses that pooled it.
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Who cites it
30 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Evolutionary dynamics and research hotspots of phage applications againstFrontiers in microbiology · 2026Pooled it
- Precision phage therapy in the AI/ML era: a systematic review of discovery-to-clinical translation evidence.Frontiers in microbiology · 2026Pooled it
- Characterization and therapeutic potential of DepZ57, a stable depolymerase targeting hypervirulent K57Applied and environmental microbiology · 2026Article
- Unraveling a new Klebsiella phage KP47 against Klebsiella spp.BMC microbiology · 2026Article
- Phenotypic heterogeneity shapes phage resistance and cocktail efficacy inMicrobiology spectrum · 2026Article
- DepoCatalog: mapping diversity of 129 recombinantly produced Klebsiella phage depolymerases.Nature communications · 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
- 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
- Stable co-existence ofmBio · 2026Article
- Effects of phage-based treatments against an OXA-48-producing Klebsiella pneumoniae isolate in simulated human gut microbiomes.BMC microbiology · 2026Article
- The Role of Genomics in Advancing and Standardising Bacteriophage Therapy.Antibiotics (Basel, Switzerland) · 2026Review
- Artificial Intelligence Applications in Bacteriophage Genomics and Host Interaction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Directed evolution of a staphylophage under biofilm and planktonic conditions.NPJ biofilms and microbiomes · 2025Article
- KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family.Nucleic acids research · 2025Article
- PDP-Miner: an AI/ML tool to detect prophage tail proteins with depolymerase domains across thousands of bacterial genomes.Bioinformatics (Oxford, England) · 2025Article
- The host range of generalist and specialist phages in capsule-diverse Klebsiella hosts is driven by the evolvability of receptor-binding proteins.PLoS biology · 2025Article
- Empathi: embedding-based phage protein annotation tool by hierarchical assignment.Nature communications · 2025Article
- Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases.Nature communications · 2025Article
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Authors and funding
7 authors.
Funding
Abstract
Bacteriophages (phages) are viruses that infect bacteria. Many of them produce specific enzymes called depolymerases to break down external polysaccharide structures. Accurate annotation and domain identification of these depolymerases are challenging due to their inherent sequence diversity. Hence, we present DepoScope, a machine learning tool that combines a fine-tuned ESM-2 model with a convolutional neural network to identify depolymerase sequences and their enzymatic domains precisely. To accomplish this, we curated a dataset from the INPHARED phage genome database, created a polysaccharide-degrading domain database, and applied sequential filters to construct a high-quality dataset, which is subsequently used to train DepoScope. Our work is the first approach that combines sequence-level predictions with amino-acid-level predictions for accurate depolymerase detection and functional domain identification. In that way, we believe that DepoScope can greatly enhance our understanding of phage-host interactions at the level of depolymerases.
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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.