But here was the deep part: Vina did not know what it was doing. It had no intent. Yet from its blind groping emerged meaning. Aris watched the first ligand descend.
And somehow—miraculously—it worked. Over 95% of Vina's predicted poses matched crystallographic reality. 3d vina
He had not. Vina's scoring function implicitly accounted for desolvation entropy. The algorithm had learned, through nothing but physics equations, that water hated being squeezed into tight spaces. But here was the deep part: Vina did
Vina had found a cluster of poses in a cleft no one had noticed—a cryptic pocket that only appeared when a specific water molecule was displaced. The predicted ΔG was -9.3. Aris watched the first ligand descend
On his screen, the protein rotated slowly: alpha helices like twisted ribbons, beta sheets like folded paper, and a deep, hydrophobic pocket where the lock of apoptosis waited for a key that no longer fit.