README.md

Serotonin Receptor (5-HT) Binding Affinity Prediction Dataset

This dataset was curated from the PDSP Ki Database to support training machine learning models that predict binding affinity (Ki in nM) of ligands to serotonin (5-HT) receptors.

Files Included

• curated_ki_database.csv: Cleaned Ki dataset filtered for 5-HT targets
• fingerprints_with_ki.csv: Molecules represented as 2048-bit Morgan (ECFP4) fingerprints
• rf_model.pkl: Trained scikit-learn RandomForestRegressor model
• test_predictions.csv: Predictions vs. actual Ki values on the test set
• train_model.ipynb: Full Jupyter notebook with training code and evaluation

Modeling Approach

• Molecules were standardized using MolVS.
• SMILES strings were converted to 2048-bit Morgan fingerprints (ECFP4) using RDKit.
• A Random Forest Regressor was trained using scikit-learn.
• The model was evaluated on a held-out 20% test set.

📈 Model Performance

• R² Score: your_R2_here
• RMSE: your_RMSE_here nM

Source

• PDSP Ki Database: https://pdsp.unc.edu/databases/kidb.php

Author

Sara Hantgan
University of Michigan | BIOINF 595 Final Project
Winter 2025