AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

AutoDock Vina is arguably one of
the fastest and most widely used
open-source programs for molecular docking. However, compared to other
programs in the AutoDock Suite, it lacks support for modeling specific
features such as macrocycles or explicit water molecules. Here, we
describe the implementation of this functionality in AutoDock Vina
1.2.0. Additionally, AutoDock Vina 1.2.0 supports the AutoDock4.2
scoring function, simultaneous docking of multiple ligands, and a
batch mode for docking a large number of ligands. Furthermore, we
implemented Python bindings to facilitate scripting and the development
of docking workflows. This work is an effort toward the unification
of the features of the AutoDock4 and AutoDock Vina programs. The source
code is available at https://github.com/ccsb-scripps/AutoDock-Vina.