JohnnyClaws/aptamer-eab-analyzer

🧬 Aptamer EAB Analyzer v5.0

ML-powered prediction tool for Electrochemical Aptamer-Based (EAB) biosensor design.

Features

• —Conformational Switch Prediction — Will your aptamer sequence work as an EAB sensor?
• —Signal Gain Estimation — Predicted % signal change
• —K-mer Embeddings — Deep sequence pattern analysis
• —Polymer Physics Engine — oxDNA-inspired end-to-end distance modeling (ΔR_ee)
• —SHAP Explainability — Understand which features drive predictions
• —Electrochemical Design — Marcus theory ET modeling, frequency optimization
• —Batch Analysis — Compare multiple sequences at once

Backends

• —ViennaRNA / seqfold for RNA secondary structure
• —XGBoost gradient boosting ensemble
• —SHAP for model interpretability
• —Custom polymer physics for conformational dynamics

Training Data

108 entries from published EAB literature (Plaxco, Arroyo-Currás, Idili, Nakatsuka, etc.)

Usage

Enter a DNA aptamer sequence and get instant predictions for EAB sensor viability.