Herein we demonstrate the use of various con-figurations of our workflow to automate the whole process of RBFE calculation: from the SMILES string for ligand representation to the final binding free energy estimate. We showcase how the steps in the workflow can be performed by both commercial and open-source software. In particular, we investigate the impact of automated docking protocols on the quality of RBFE predictions, comparing the performance of both open-source and commercial docking engines, and further demonstrate the deployment of the workflow on both in-house and cloud compute platforms.