LEMONS

LEMONS enumerates hypothetical modular natural product structures and evaluates molecular similarity methods to characterize natural-product chemical space and support microbial genome mining.

Key Features:

• Modular natural product enumeration: Enumerates hypothetical modular natural product structures to generate candidate molecules within natural-product chemical space.
• Molecular similarity comparison: Conducts comparative analysis of various molecular similarity methods specifically tailored for natural products.
• Controlled synthetic data analyses: Generates and analyzes controlled synthetic datasets to study how biosynthetic parameters influence similarity searches.
• Natural product retrobiosynthesis and alignment: Implements a recently described algorithm for natural product retrobiosynthesis and alignment.
• Performance benchmarking against 2D fingerprints: Compares results to conventional two-dimensional fingerprints and can outperform them when rule-based retrobiosynthesis is applicable.
• Targeted chemical-space exploration: Facilitates targeted exploration of natural-product chemical space for hypothesis-driven analyses.

Scientific Applications:

• Molecular similarity benchmarking: Benchmarking and performance analysis of molecular similarity methods for natural products.
• Chemical-space exploration: Exploration and enumeration of potential natural-product configurations within unique chemical space.
• Microbial genome mining: Supporting targeted investigations in microbial genome mining by linking biosynthetic logic to candidate structures.
• Assessment of biosynthetic parameter effects: Studying how variation in biosynthetic parameters affects similarity search outcomes.
• Support for drug discovery: Enabling analyses relevant to natural-product-based lead identification and drug discovery research.

Methodology:

Enumeration of modular natural product structures, generation and analysis of controlled synthetic datasets to vary biosynthetic parameters, application of a recently described natural product retrobiosynthesis and alignment algorithm, and comparison against conventional two-dimensional fingerprint methods (including rule-based retrobiosynthesis comparisons).