ArticleNucleic acids research2023
ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 27 citations in OpenAlex.
- Engineered polyketide synthases enable a microbial chassis for recyclable plastics with tunable properties.Nature biotechnology · 2026Article
- Evolution, structure and function of the putative biosynthetic gene cluster of the fungal secondary metabolite myriocin, a potent inhibitory sphingolipid.Communications biology · 2026Article
- Engineering an Extremely Hybrid PKS for Adipic Acid Production.ACS synthetic biology · 2026Article
- TridentSynth: a webtool for the retrosynthesis of molecules using chimeric type I polyketide synthases and chemoenzymatic pathways.Nucleic acids research · 2026Article
- StreptoCAD: An Open-Source Software Toolbox Automating Genome Engineering Workflows in Streptomycetes.ACS synthetic biology · 2025Article
- Engineering Polyketide Stereocenters with Ketoreductase Domain Exchanges.Journal of the American Chemical Society · 2025Article
- Merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis.Nature communications · 2025Article
- Novel Gene Clusters for Secondary Metabolite Synthesis in Mesophotic Sponge-Associated Bacteria.Microbial biotechnology · 2025Article
- Repurposing a Fully Reducing Polyketide Synthase toward 2-Methyl Guerbet-like Lipids.ACS catalysis · 2024Article
- Seamless site-directed mutagenesis in complex cloned DNA sequences using the RedEx method.Nature protocols · 2024Review
- Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products.Natural product reports · 2024Review
- RAIChU: automating the visualisation of natural product biosynthesis.Journal of cheminformatics · 2024Article
- Enzyme Databases in the Era of Omics and Artificial Intelligence.International journal of molecular sciences · 2023Review
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Megasynthase enzymes such as type I modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) play a central role in microbial chemical warfare because they can evolve rapidly by shuffling parts (catalytic domains) to produce novel chemicals. If we can understand the design rules to reshuffle these parts, PKSs and NRPSs will provide a systematic and modular way to synthesize millions of molecules including pharmaceuticals, biomaterials, and biofuels. However, PKS and NRPS engineering remains difficult due to a limited understanding of the determinants of PKS and NRPS fold and function. We developed ClusterCAD to streamline and simplify the process of designing and testing engineered PKS variants. Here, we present the highly improved ClusterCAD 2.0 release, available at https://clustercad.jbei.org. ClusterCAD 2.0 boasts support for PKS-NRPS hybrid and NRPS clusters in addition to PKS clusters; a vastly enlarged database of curated PKS, PKS-NRPS hybrid, and NRPS clusters; a diverse set of chemical 'starters' and loading modules; the new Domain Architecture Cluster Search Tool; and an offline Jupyter Notebook workspace, among other improvements. Together these features massively expand the chemical space that can be accessed by enzymes engineered with ClusterCAD.
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