ArticleViruses2022
Identification of Phage Receptor-Binding Protein Sequences with Hidden Markov Models and an Extreme Gradient Boosting Classifier.
Article in Viruses, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 2 of them syntheses that pooled it.
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Who cites it
36 citing papers in PubMed, 2 syntheses or guidelines pooled it, 56 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
- From genomic signals to prediction tools: a critical feature analysis and rigorous benchmark for phage-host prediction.Briefings in bioinformatics · 2025Pooled it
- Isolation and characterization of broad-rangeMicrobiology (Reading, England) · 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
- In silico exploration of the genomic repertoire of Iranian aquatic bacteria: Prophage carriage, bioactive compound potential, CRISPR-Cas immunity, and integrated defensive-metabolic islands.Biochemistry and biophysics reports · 2026Article
- Genomic landscape of biosynthetic gene clusters in Iranian extremophiles reveals prolific metabolite potential, prophage associations, and integrated defensive-metabolic islands.BMC microbiology · 2026Article
- Towards accurate artificial intelligence models for strain-level phage-host prediction.Briefings in bioinformatics · 2026Article
- Genome-based taxonomic classification ofFrontiers in microbiology · 2026Article
- Directed evolution of a staphylophage under biofilm and planktonic conditions.NPJ biofilms and microbiomes · 2025Article
- Phage-mediated control of melioidosis in Southern China: molecular insights and therapeutic potential of N4-like viruses from Hainan.BMC microbiology · 2025Article
- Host-specificity and therapeutic potential of novel Escherichia coli-targeting bacteriophages for bovine mastitis control.Scientific reports · 2025Article
- KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family.Nucleic acids research · 2025Article
- Evaluating the therapeutic potential of a novel bacteriophage cocktail against carbapenem-resistant Pseudomonas aeruginosa in a murine burn wound infection model.BMC microbiology · 2025Article
- Empathi: embedding-based phage protein annotation tool by hierarchical assignment.Nature communications · 2025Article
- Article
- Phage and Endolysin Therapy Against Antibiotics Resistant Bacteria: From Bench to Bedside.MedComm · 2025Review
- RBPseg: Toward a complete phage tail fiber structure atlas.Science advances · 2025Article
- Dual Nature of Bacteriophages: Friends or Foes in Minimally Processed Food Products-A Comprehensive Review.Viruses · 2025Review
- Amino acid residues in the tail fiber differentiate the host specificity ofJournal of virology · 2025Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Receptor-binding proteins (RBPs) of bacteriophages initiate the infection of their corresponding bacterial host and act as the primary determinant for host specificity. The ever-increasing amount of sequence data enables the development of predictive models for the automated identification of RBP sequences. However, the development of such models is challenged by the inconsistent or missing annotation of many phage proteins. Recently developed tools have started to bridge this gap but are not specifically focused on RBP sequences, for which many different annotations are available. We have developed two parallel approaches to alleviate the complex identification of RBP sequences in phage genomic data. The first combines known RBP-related hidden Markov models (HMMs) from the Pfam database with custom-built HMMs to identify phage RBPs based on protein domains. The second approach consists of training an extreme gradient boosting classifier that can accurately discriminate between RBPs and other phage proteins. We explained how these complementary approaches can reinforce each other in identifying RBP sequences. In addition, we benchmarked our methods against the recently developed PhANNs tool. Our best performing model reached a precision-recall area-under-the-curve of 93.8% and outperformed PhANNs on an independent test set, reaching an F1-score of 84.0% compared to 69.8%.
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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.