RxnSim

RxnSim quantifies chemical reaction similarity using molecular signatures of participating molecules to compare substrates and products, classify reactions, and identify candidate enzymes.

Key Features:

• Molecular signatures: Represents participating molecules with molecular signatures for quantitative similarity assessment.
• Substrate, product and transformation comparison: Evaluates similarities between substrates and products as well as their chemical transformations.
• Weighted similarity and masking: Performs weighted similarity computations with user-defined masking of specific chemical moieties.
• R implementation: Implemented in R for incorporation into computational workflows.

Scientific Applications:

• Reaction similarity search: Enables retrieval of similar reactions for database searches and comparative analyses.
• Reaction classification: Supports classification of reactions based on computed similarity metrics.
• Enzyme candidate identification: Facilitates identification of candidate enzymes associated with similar reactions.
• Pathway and enzymatic research: Supports exploration of enzyme function and the development of novel biochemical pathways.

Methodology:

Computes similarity using molecular signatures to compare substrates, products, and transformations; applies weighted similarity via user-defined masking of chemical moieties; implemented in R.