Enabling performance portability on the LiGen drug discovery pipeline
Sep 1, 2024
muDock
Molecular docking is a well-known problem in scientific literature. It aims to estimate the 3D displacement of a molecule with a small molecular weight, named ligand, when it interacts with the target protein. The main issue is the number of degree of freedom involved in the operation. Due to the difference in size between the protein and ligand, we need to find the correct position and orientation of the ligand inside a pocket cavity. Moreover, the molecules are not rigid bodies, but we can rotate a subset of their bonds, changing their geometry, without changing their chemical and physical properties. Thus, we have six degrees of freedom for rigid rototranslations in a 3D space and one additional degree of freedom for each of those bonds. Arguably, the most popular tool that performs molecular docking is autodock (https://autodock.scripps.edu/). Its implementation is composed of a feature rich ecosystem of tools, that might employ different optimization strategies to solve the exploration problem.
Jun 1, 2024