Machine learning-enabled retrobiosynthesis of molecules

T Yu, AG Boob, MJ Volk, X Liu, H Cui, H Zhao - Nature Catalysis, 2023 - nature.com
Retrobiosynthesis provides an effective and sustainable approach to producing functional
molecules. The past few decades have witnessed a rapid expansion of biosynthetic …

Designing microbial cell factories for the production of chemicals

JS Cho, GB Kim, H Eun, CW Moon, SY Lee - Jacs Au, 2022 - ACS Publications
The sustainable production of chemicals from renewable, nonedible biomass has emerged
as an essential alternative to address pressing environmental issues arising from our heavy …

RetroBioCat as a computer-aided synthesis planning tool for biocatalytic reactions and cascades

W Finnigan, LJ Hepworth, SL Flitsch, NJ Turner - Nature catalysis, 2021 - nature.com
As the enzyme toolbox for biocatalysis has expanded, so has the potential for the
construction of powerful enzymatic cascades for efficient and selective synthesis of target …

Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP

S Zheng, T Zeng, C Li, B Chen, CW Coley… - Nature …, 2022 - nature.com
The complete biosynthetic pathways are unknown for most natural products (NPs), it is thus
valuable to make computer-aided bio-retrosynthesis predictions. Here, a navigable and user …

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals

P Carbonell, AJ Jervis, CJ Robinson, C Yan… - Communications …, 2018 - nature.com
The microbial production of fine chemicals provides a promising biosustainable
manufacturing solution that has led to the successful production of a growing catalog of …

[HTML][HTML] Automating the design-build-test-learn cycle towards next-generation bacterial cell factories

N Gurdo, DC Volke, D McCloskey, PI Nikel - New Biotechnology, 2023 - Elsevier
Automation is playing an increasingly significant role in synthetic biology. Groundbreaking
technologies, developed over the past 20 years, have enormously accelerated the …

Machine learning modeling of family wide enzyme-substrate specificity screens

S Goldman, R Das, KK Yang… - PLoS computational …, 2022 - journals.plos.org
Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex
natural products, and commodity chemicals at scale. However, the adoption of biocatalysis …

Getting the Most Out of Enzyme Cascades: Strategies to Optimize In Vitro Multi-Enzymatic Reactions

R Siedentop, C Claaßen, D Rother, S Lütz… - Catalysts, 2021 - mdpi.com
In vitro enzyme cascades possess great benefits, such as their synthetic capabilities for
complex molecules, no need for intermediate isolation, and the shift of unfavorable equilibria …

The isoprenoid alcohol pathway, a synthetic route for isoprenoid biosynthesis

JM Clomburg, S Qian, Z Tan… - Proceedings of the …, 2019 - National Acad Sciences
The more than 50,000 isoprenoids found in nature are all derived from the 5-carbon
diphosphates isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) …

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives

J Hafner, J Payne, H MohammadiPeyhani… - Nature …, 2021 - nature.com
Plant natural products (PNPs) and their derivatives are important but underexplored sources
of pharmaceutical molecules. To access this untapped potential, the reconstitution of …