ReactPRED

ReactPRED predicts and analyzes biochemical reactions and generates reaction rule sets to support engineered metabolic pathway design.

Key Features:

• Automated reaction rule generation: Automatically creates reaction rule sets from user-defined reaction collections.
• Reaction prediction: Predicts feasible biochemical transformations within and between metabolic pathways.
• Parameter tuning: Allows adjustment of reaction rule degree and tolerance levels to tune specificity and sensitivity of predictions.
• In silico screening support: Enables in silico screening of reaction and pathway spaces to identify routes for synthesizing or degrading target chemicals.
• Rule-set scalability: Automates rule creation to overcome constraints of manually curated and application-specific rule sets.

Scientific Applications:

• Pathway engineering: Design and evaluation of synthetic metabolic pathways for synthesis or degradation of target chemicals.
• In silico pathway screening: High-throughput screening of reaction networks to identify feasible transformation routes.
• Metabolic modeling support: Generation of reaction rule sets for incorporation into downstream metabolic network analyses.
• Prediction refinement: Tuning of prediction specificity and sensitivity for pathway design and optimization studies.

Methodology:

Creates reaction rule sets from user-defined reaction collections, applies those rules to predict feasible biochemical transformations, and refines predictions by adjusting reaction rule degree and tolerance levels.