ArticleJACS Au2026
PARAS: High-Accuracy Machine Learning of Substrate Specificities in Nonribosomal Peptide Synthetases.
Article in JACS Au, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
- Tandem-sgRNA Provides an Effective Reverse Genetic Approach for Suppression of Streptomyces Biosynthetic Gene Clusters and Secondary Metabolism.ACS synthetic biology · 2026Article
- Heterologous expression of NRPS and PKS pathways in Escherichia coli: from bottlenecks to biosynthetic platforms.Essays in biochemistry · 2026Review
- Nerpa 2: probabilistic linking of biosynthetic gene clusters to nonribosomal peptides.Bioinformatics (Oxford, England) · 2026Article
- DeepAden: an explainable machine learning method for predicting the substrate specificity of nonribosomal peptide synthetases.Nucleic acids research · 2026Article
- PhyloNaP: a user-friendly database of phylogeny for natural product-producing enzymes.Bioinformatics (Oxford, England) · 2026Article
- Discovery of actinomycin derivatives with improved selectivity against malaria parasites from a Streptomyces culture library.The Journal of antibiotics · 2026Article
- Discovery of the 5-Chlorokynurenine Pathway in Lodopyridone Biosynthesis.Journal of natural products · 2026Article
- Fusaric Acid Analogs and Dimers from Marine-DerivedJournal of natural products · 2026Article
- Discovery and Biosynthesis of the Novel Glycotetrapeptide Antibiotic Biffamycin A.Angewandte Chemie (International ed. in English) · 2026Article
- Shared biosynthetic architectures generate diverse β-amino polyketide residues in cyanobacterial peptides.bioRxiv : the preprint server for biology · 2026Article
- Heterologous Production of Barnesin A, an NRPS-PKS Hybrid Containing a Rare Vinylogous Arginine Moiety.Chembiochem : a European journal of chemical biology · 2026Article
- Modular biosynthesis of microbiome-derived polyketides and nonribosomal peptides: insights and opportunities for Lactobacillaceae.Microbial cell factories · 2026Review
- Membrane Vesicle-Mediated Delivery of Antibacterial Lipopeptides byACS chemical biology · 2026Article
- Genetic Dereplication of MultipleJournal of natural products · 2026Article
- Paenidepsins are a Family of Lipopeptides fromJournal of natural products · 2026Article
- An integrative chemical and genomic similarity approach linking fungal secondary metabolites and biosynthetic gene clusters.Organic & biomolecular chemistry · 2026Article
- The Biosynthetic Gene Cluster of Boydines in Scedosporium apiospermum.Mycopathologia · 2026Article
- Benchmarking methods for measuring biosynthetic gene cluster similarity and determination of gene cluster families.Bioinformatics (Oxford, England) · 2025Article
- Coniontins, lipopetaibiotics active against Candida auris identified from a microbial natural product fractionation library.Nature communications · 2025Article
- Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity.Nucleic acids research · 2025Article
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Authors and funding
18 authors.
Funding
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Abstract
Nonribosomal peptides are diverse natural products with important applications in medicine and agriculture. Bacterial and fungal genomes contain thousands of nonribosomal peptide biosynthetic gene clusters (BGCs) of unknown function, providing a promising resource for peptide discovery. Core structural features of such peptides can be inferred by predicting the substrate(s) of adenylation (A) domains in nonribosomal peptide synthetases (NRPSs). However, existing approaches to A domain prediction rely on limited data sets and often struggle with domains selecting large substrates and domains from underrepresented taxa. Here, we systematically curate and computationally analyze 3653 A domains and present two high-accuracy specificity predictors, PARAS and PARASECT. A type of A domain with unusually high l-tryptophan specificity was identified through the application of PARAS. Cloning and expression of the biosynthetic gene cluster encoding the NRPS showed that it directs the biosynthesis of tryptopeptin-related metabolites in
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