A Performance and Energy Evaluation of OpenCL-accelerated Molecular Docking

Molecular Docking is a methodology used extensively in modern drug design. It aims to predict the binding position of two molecules by calculating the energy of their possible binding poses. One of the most cited docking tools is AutoDock. At its core, it solves an optimization problem by generating a large solution space of possible poses, and searches among them for the one having the lowest energy. These complex algorithms thus benefit from parallelization based run-time acceleration. This work presents an OpenCL implementation of AutoDock, and a corresponding performance evaluation on two different platforms based on multi-core CPU and GPU accelerators. It shows that OpenCL allows highly efficient docking simulations, achieving speedups of ~4x and ~56x over the original serial AutoDock version, as well as energy efficiency gains of ~2x and ~6x. respectively. To the best of our knowledge, this work is the first one also considering the energy efficiency of molecular docking programs.