Novopathfinder

NovoPathFinder is a powerful web server for designing novel metabolic pathways in metabolic engineering and synthetic biology. It enables researchers to computationally construct biosynthetic routes for valuable chemicals, significantly expanding the potential of microbial cell factories.

The tool offers unique features: it designs pathways between specified molecules independent of host organisms; automatically constructs heterologous pathways within E. coli or yeast models using known or novel reactions without requiring predefined precursors; and comprehensively evaluates pathway feasibility using criteria like enzyme promiscuity scores, thermodynamic analysis, theoretical yield, pathway length, and intermediate toxicity (LD50). This evaluation integrates with Genome-Scale Metabolic (GEM) models for real-time yield calculations under custom conditions.

novoPathFinder excels at recovering experimentally validated pathways more effectively than other rule-based tools and identifies novel, often shorter or more efficient, pathways for further experimental exploration. Demonstrated success cases include pathways for vanillin, lycopene, artemisinic acid, and cannabidiol, showcasing its ability to drive innovation in bioproduction.