Inverse docking method for new proteins targets identification: A parallel approach

• 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.