Top 5 Scaffold‑Split QSAR Hits for EGFR Inhibitor Discovery: A Random Forest Co‑Scientist
TL;DR – Technical Takeaways Scaffold splitting trumps random splits for kinase inhibitor models—without it, your QSAR will lie to you. We built a Random Forest model on ChEMBL data, using RDKit descriptors and BRICS fragmentation. SHAP waterfall plots exposed which molecular fragments drive pIC50, linking structure to activity. The pipeline runs as a Kedro‑wrapped co‑scientist inside a container that a chemist can interrogate via a REST endpoint. We’ll share the top 5 predicted EGFR inhibitors our model surfaced—molecules never tested against EGFR in the training set. We’ve been burned before by a “world‑class” QSAR model that hit R² = 0.89 on random cross‑validation, only to crash to R² = 0.21 when we tested it on a new chemical series. The sin? Random splitting. In kinase‑centric projects like EGFR inhibitor discovery, random splits create artificially high performance by leaking close analogs across folds. That’s why we pivoted to a scaffold‑split QSAR method —a ...