ArticleNature communications2024
Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Metabolite-mediated plant immunity: From traditional defenders to artificial elicitors.Journal of integrative plant biology · 2026Review
- Deciphering the Function and Structure of PA1216 as an S-Adenosyl-l-Methionine Binding Protein Using Differential Scanning Fluorimetry and Circular Dichroism.Protein science : a publication of the Protein Society · 2026Article
- Combating Antibacterial Resistance: The Integrative Role of Artificial Intelligence in Bio-Based Product Development.Antibiotics (Basel, Switzerland) · 2026Review
- Genomic insights into novelBurkholderia sp. Bmkn7 from coastal saline-affected rice fields unveils potential antimicrobial metabolites and plant growth-promoting traits.Scientific reports · 2026Article
- BGC-MAC and BGC-MAP: Attention-Based Models for Biosynthetic Gene Cluster Classification and Product Matching.Journal of chemical information and modeling · 2026Article
- Research progress of glutarimide-containing polyketides: Structures, bioactivities and their biosynthesis.Pharmaceutical science advances · 2025Review
- Emerging strategies to enhance microbial natural product-based drug discovery.Current opinion in biotechnology · 2025Review
- Seq2Saccharide: Discovering Oligosaccharides and Aminoglycosides Natural Products by Integrating Computational Mass Spectrometry and Genome Mining.Journal of the American Chemical Society · 2025Article
- antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation.Nucleic acids research · 2025Article
- The Deep Mining Era: Genomic, Metabolomic, and Integrative Approaches to Microbial Natural Products from 2018 to 2024.Marine drugs · 2025Review
- Multi-Omics Analysis of Gut Microbiome and Host Metabolism in Different Populations of Chinese Alligators (Ecology and evolution · 2025Article
- Interpretable adenylation domain specificity prediction using protein language models.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
20 authors.
Funding
Abstract
Type 1 polyketides are a major class of natural products used as antiviral, antibiotic, antifungal, antiparasitic, immunosuppressive, and antitumor drugs. Analysis of public microbial genomes leads to the discovery of over sixty thousand type 1 polyketide gene clusters. However, the molecular products of only about a hundred of these clusters are characterized, leaving most metabolites unknown. Characterizing polyketides relies on bioactivity-guided purification, which is expensive and time-consuming. To address this, we present Seq2PKS, a machine learning algorithm that predicts chemical structures derived from Type 1 polyketide synthases. Seq2PKS predicts numerous putative structures for each gene cluster to enhance accuracy. The correct structure is identified using a variable mass spectral database search. Benchmarks show that Seq2PKS outperforms existing methods. Applying Seq2PKS to Actinobacteria datasets, we discover biosynthetic gene clusters for monazomycin, oasomycin A, and 2-aminobenzamide-actiphenol.
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