rp2paths

rp2paths performs automated retrosynthetic search to design metabolic pathways by applying generalized reaction rules to explore enzyme-accessible chemical space and identify biosynthetic routes from a chassis organism to a desired target compound.

Key Features:

• Generalized reaction rules: Uses generalized reaction rules derived from known biochemical transformations to model possible enzymatic reactions.
• Enzyme-accessible chemical space exploration: Systematically explores enzyme-accessible chemical space to identify feasible conversion steps toward target compounds.
• Combinatorial expansion control: Constrains combinatorial expansion to efficiently enumerate pathway candidates while maintaining control over search scope and tractability.
• Integration with bioinformatics and cheminformatics tools: Integrates bioinformatics and cheminformatics tools to generate, filter, and evaluate alternative biosynthetic routes.
• Enzyme promiscuity and substrate compatibility: Accounts for enzyme promiscuity and substrate compatibility during route generation and evaluation.
• Reproducible and scalable predictions: Produces reproducible and scalable retrosynthesis predictions suitable for metabolic engineering pipelines.

Scientific Applications:

• Metabolic pathway design: Designs biosynthetic pathways in synthetic and industrial biotechnology to connect a chassis organism to a desired target compound.
• Biosensor development: Supports identification of detectable intermediates and sensing-linked pathways for biosensor design.
• Metabolic rewiring: Proposes alternative enzymatic routes and pathway variants to enable metabolic rewiring.
• Design–build–test–learn cycles: Provides rapid retrosynthesis predictions to inform iterative design–build–test–learn cycles in strain engineering.
• Novel production pathways: Suggests candidate pathways for production of next-generation compounds.

Methodology:

Applies generalized reaction rules derived from known biochemical transformations, systematically explores enzyme-accessible chemical space, constrains combinatorial expansion to enumerate pathway candidates, integrates bioinformatics and cheminformatics tools to generate, filter, and evaluate alternative biosynthetic routes, and incorporates enzyme promiscuity and substrate compatibility in route evaluation.