The first time they ran a benchmark, the results were almost unbelievable. A docking run that used to take twelve minutes on AutoDock 4 completed in forty seconds with the new engine. And the accuracy—measured by how well it reproduced known crystal structures—was slightly better . Forli ran it again. Then again. Each time, the same result: a hundredfold speedup, no loss of fidelity.
They named it AutoDock Vina—"Vina" for "vine," suggesting something that grows quickly and finds its way. autodock vina
Dr. Stefano Forli, an Italian computational chemist with a passion for elegant code, and Dr. Garrett Morris, a methodical scientist with a background in physics, inherited a legacy tool: AutoDock 4. It was powerful but notoriously slow. A single docking simulation could take minutes, even hours, and screening a library of a hundred thousand drug-like molecules against a protein target could consume weeks of supercomputer time. Forli would stare at the logs, watching the genetic algorithms churn through thousands of conformations, feeling the weight of every unnecessary calculation. "There has to be a faster way," he told Morris one evening, pointing at a graph of the scoring function. "The energy landscape is rugged, but our search path is full of detours." The first time they ran a benchmark, the