3d Vina Here

On screen, the small molecule tumbled end over end—a benzofuran derivative with a nitrogen spike. Vina calculated the free energy of binding: ΔG. Negative numbers were good. -6.2 kcal/mol. Not great.

Vina did not see molecules the way a chemist does. It saw and degrees of freedom . It imagined each ligand (the drug candidate) as a rigid body with rotatable bonds, then dropped it into the 3D grid of the protein like a key thrown into a dark room. 3d vina

A senior reviewer frowned. "But you don't know why it binds so tightly. Not really." On screen, the small molecule tumbled end over

Vina's 3D grid averaged all that motion into a frozen sculpture. Then it searched. It saw and degrees of freedom

At iteration 27, the molecule slipped into the hydrophobic pocket like a key turned in a lock long rusted shut. Hydrogen bonds snapped into place. A pi-stack with a phenylalanine residue. A perfect van der Waals embrace.

The molecule kissed the protein's surface and bounced off.