ArticleNucleic acids research2018
ClusterCAD: a computational platform for type I modular polyketide synthase design.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 64 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
- Graph neural networks can predict ketosynthase substrate specificity.Scientific reports · 2026Article
- De novo design of ribosomally synthesized and post-translationally modified peptides.Nature chemistry · 2025Article
- Repurposing a Fully Reducing Polyketide Synthase toward 2-Methyl Guerbet-like Lipids.ACS catalysis · 2024Article
- Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products.Natural product reports · 2024Review
- Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase.Journal of the American Chemical Society · 2023Article
- ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design.Nucleic acids research · 2023Article
- Metabolic pathway assembly using docking domains from type I cis-AT polyketide synthases.Nature communications · 2022Article
- Biosynthetic pathways of triterpenoids and strategies to improve their Biosynthetic Efficiency.Plant growth regulation · 2022Review
- Mining genomes to illuminate the specialized chemistry of life.Nature reviews. Genetics · 2021Review
- Microbial natural product databases: moving forward in the multi-omics era.Natural product reports · 2021Review
- RedEx: a method for seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters.Nucleic acids research · 2020Article
- Site directed mutagenesis as a precision tool to enable synthetic biology with engineered modular polyketide synthases.Synthetic and systems biotechnology · 2020Review
- Biosynthesis of aromatic polyketides in microorganisms using type II polyketide synthases.Microbial cell factories · 2020Review
- Review
- Computational Tools for Discovering and Engineering Natural Product Biosynthetic Pathways.iScience · 2020Review
- MIBiG 2.0: a repository for biosynthetic gene clusters of known function.Nucleic acids research · 2020Article
- Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters inComputational and structural biotechnology journal · 2020Review
- Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis.Frontiers in molecular biosciences · 2020Review
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ClusterCAD is a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKS chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.
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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.