Generally, when the binding site of a protein is known and a molecule is similar to known ligands, traditional docking methods are rather accurate in the prediction of the interaction. Unfortunately, when the binding site is unknown, the blind docking analysis requires large computational resources and the results are usually not accurate.
Yada is a new tool for molecular docking that is capable to distribute efficiently calculations onto general purposes computer grid and that combines biological and structural information of the receptor. Yada is available for Windows and Linux.
Piotto, S., Di Biasi, L., Fino, R., Parisi, R., & Sessa, L. (2016). Yada: a novel tool for molecular docking calculations. Journal of computer-aided molecular design, 30(9), 753-759.