•A framework to perform inverse docking was developed.•Different strategies to distribute the docking procedure were implemented.•Validation with experimental complex have been done.•A docking test of one ligand versus 100 proteins was performed.•A better conformational sampling is processed than current methods. Molecular docking is a widely used computational technique that allows studying structure-based interactions complexes between biological objects at the molecular scale. The purpose of the current work is to develop a set of tools that allows performing inverse docking, i.e., to test at a large scale a chemical ligand on a large dataset of proteins, which has several applications on the field of drug research. We developed different strategies to parallelize/distribute the docking procedure, as a way to efficiently exploit the computational performance of multi-core and multi-machine (cluster) environments. The experiments conducted to compare these different strategies encourage the search for decomposing strategies since it improves the execution of inverse docking.