Accelerating a Geometric Approach to Molecular Docking with OpenACC

In a drug discovery process, the Molecular Docking task aims at estimating the three-dimensional pose of a molecule when it interacts with the target protein. This task is usually used to perform a screening on a large library of molecules to find the most promising candidates. The output of this task is used to estimate the actual strength of atomic interactions. In this document we focus on an application that performs molecular docking using geometrical features of the molecule and of the protein, to quickly screen the target chemical library. Due to the size of the chemical library and to the complexity of the task, the application is a typical batch job that runs in an HPC platform, optimized for CPU processing. Given the amount of parallelism of this application, we evaluate the possibility to run such application on a GPU node, leveraging the OpenACC directive language. Preliminary results show that we are able to achieve a significant speedup on the kernel that was the bottleneck on the CPU (up to 16x), while we achieve a speedup of 5x on the overall execution.