RDT

RDT extracts and analyzes chemical features from biochemical reactions to identify Atom-Atom Mapping (AAM), Bond Changes (BCs), and Reaction Centres for characterization of enzymatic transformations.

Key Features:

• Atom-Atom Mapping (AAM): Computes atom-level correspondences between reactants and products to track individual atom transformations.
• Bond Changes (BCs): Detects and reports changes in chemical bonds occurring during reactions to reveal mechanistic alterations.
• Reaction Centres: Identifies molecular regions where significant chemical changes occur within a reaction.
• Standard Format Support (RXN/SMILES): Accepts and processes chemical input/output in RXN and SMILES formats.
• Visualization Capabilities: Generates images that represent mapped reactions and annotated bond changes.
• High-accuracy AAM and BC detection: Produces precise AAM results and highlights BCs as described in the original implementation.

Scientific Applications:

• Metabolic Pathway Analysis: Extracts detailed chemical features from biochemical reactions to support analysis of metabolic pathways and enzymatic processes.
• Comparative Reaction Studies: Enables comparison of mapped reactions and annotated bond changes for studies in drug discovery and synthetic biology.

Methodology:

Implemented in Java; computes Atom-Atom Mapping (AAM), detects and highlights Bond Changes (BCs), identifies Reaction Centres, accepts RXN/SMILES input, and generates images representing mapped reactions.