ArticleNature communications2018
Pathway design using de novo steps through uncharted biochemical spaces.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
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Who cites it
37 citing papers in PubMed.
- TridentSynth: a webtool for the retrosynthesis of molecules using chimeric type I polyketide synthases and chemoenzymatic pathways.Nucleic acids research · 2026Article
- Mechanism-informed rules tunably balance novelty and feasibility of predicted enzymatic reactions.bioRxiv : the preprint server for biology · 2026Article
- MechFind: a computational framework for de novo prediction of enzyme mechanisms.Nature communications · 2026Article
- Stoichiometrically Engineered Hydrated Ionic Liquids Enabling Reinforcement of Enzyme Cascade with Improved Thermodynamic Stability.ACS sustainable chemistry & engineering · 2026Article
- MechFind: A computational framework for de novo prediction of enzyme mechanisms.bioRxiv : the preprint server for biology · 2025Article
- Computational tools for nonnatural pathway design: Algorithms, applications, and challenges.Biodesign research · 2025Review
- From reactants to products: computational methods for biosynthetic pathway design.Synthetic and systems biotechnology · 2025Review
- novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection.PLoS computational biology · 2025Article
- Fermi calculations enable quick downselection of target genes and process optimization in photosynthetic systems.Plant physiology · 2025Review
- Merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis.Nature communications · 2025Article
- Comprehensive evaluation of the capacities of microbial cell factories.Nature communications · 2025Article
- minChemBio: Expanding Chemical Synthesis with Chemo-Enzymatic Pathways Using Minimal Transitions.ACS synthetic biology · 2025Article
- CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters.Nature communications · 2025Article
- Computational approaches for enteric methane mitigation research: from fermi calculations to artificial intelligence paradigms.Animal frontiers : the review magazine of animal agriculture · 2024Article
- Design and construction of artificial metabolic pathways for the bioproduction of useful compounds.Plant biotechnology (Tokyo, Japan) · 2024Article
- Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review.ACS synthetic biology · 2024Article
- REME: an integrated platform for reaction enzyme mining and evaluation.Nucleic acids research · 2024Article
- Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota.NPJ systems biology and applications · 2024Article
- An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification.Journal of cheminformatics · 2023Article
- Biotechnological Plastic Degradation and Valorization Using Systems Metabolic Engineering.International journal of molecular sciences · 2023Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Existing retrosynthesis tools generally traverse production routes from a source to a sink metabolite using known enzymes or de novo steps. Generally, important considerations such as blending known transformations with putative steps, complexity of pathway topology, mass conservation, cofactor balance, thermodynamic feasibility, microbial chassis selection, and cost are largely dealt with in a posteriori fashion. The computational procedure we present here designs bioconversion routes while simultaneously considering any combination of the aforementioned design criteria. First, we track and codify as rules all reaction centers using a prime factorization-based encoding technique (rePrime). Reaction rules and known biotransformations are then simultaneously used by the pathway design algorithm (novoStoic) to trace both metabolites and molecular moieties through balanced bio-conversion strategies. We demonstrate the use of novoStoic in bypassing steps in existing pathways through putative transformations, assembling complex pathways blending both known and putative steps toward pharmaceuticals, and postulating ways to biodegrade xenobiotics.
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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.