Core scaffold Hydrophobic pocket H-bond donor residue Acidic residue (Asp102⁻)
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Fragment-Based Drug Design: Growth-Vector Lead Optimization

Drug design rarely starts from scratch — medicinal chemists usually begin with a small core fragment already known to bind a target, then grow it outward into neighbouring pockets to gain potency. This simulator renders a receptor pocket in 3D with three distinct chemical environments — a hydrophobic patch, an H-bond donor residue, and a negatively charged residue — and lets you attach a functional group at each growth vector from the core scaffold. Every choice is scored by real medicinal-chemistry logic: chemical complementarity between the group and the pocket, a steric clash penalty for oversized groups, and a running Lipinski Rule-of-Five check, so you can watch predicted binding free energy climb even as drug-likeness degrades — the exact trade-off that drives real lead optimization.