Vina
AutoDock Vina docking engine used for fast protein-ligand pose and affinity screening.
Local Relevance
In the STRC work, Vina is useful as a fast screening axis, but only when ligand preparation and receptor rigidity assumptions are explicit. The Vina Ligand Prep — Gasteiger Zero-Anion Artifact and Dimorphite-Meeko Fix note captures the main failure mode: default preparation can erase formal anion charges and make rank comparisons misleading.
Use With Caveats
Treat Vina scores as one model output, not truth. Cross-check charge-sensitive ligands with formal-charge prep, Meeko, Dimorphite-DL, and flexible-method evidence when the binding pocket requires induced fit.