About AutoDock Vina
AutoDock Vina (Vina) is one of the docking engines in the AutoDock Suite, together with AutoDock4 (AD4), AutoDockGPU, AutoDockFR, and AutoDock-CrankPep, and arguably among the most widely used and successful docking engines. The reasons for this success are mostly due to its ease of use and its speed (up to 100x faster than AD4), when compared to the other docking engines in the suite and elsewhere, as well as being open source. The source code is available at https://github.com/ccsb-scripps/AutoDock-Vina.
Research groups around the world have modified and built upon the Vina source code, improving the search algorithm (QuickVina2), made the interface more user friendly and allow modification of scoring terms through the user interface (Smina), and improved the scoring function for carbohydrate docking (Vina-Carb), halogen bonds (VinaXB) and created an improved scoring function (Vinardo).
Over the years many specialized docking methods were developed for AutoDock 4 but were never ported to AutoDock Vina. This happened because AutoDock 4 allows the user to modify a large number of docking parameters, providing direct access to some of the engine internals, with benefits in terms of flexibility and adaptability. Conversely, the Vina code is highly optimized and specialized, and one of its hallmarks is the very limited amount of user input necessary to perform a docking, making it harder to implement additional functionality, which requires changes to the source code. However, some of the specialized docking methods are now available in Vina (v1.2.x) such as macrocyclic flexibility, specialized metal coordination models, explicit waters hydrated and simultaneous docking of multiple ligands. Vina was further extended by adding Python bindings to facilitate programmatic access to the docking engine functions.