Benchmarking the Performance of Irregular Computations in AutoDock-GPU Molecular Docking.

ABSTRACT: Irregular applications can be found in different scientific fields. In computer-aided drug design, molecular docking simulations play an important role in finding promising drug candidates. AutoDock is a software application widely used for predicting molecular interactions at close distances. It is characterized by irregular computations and long execution runtimes. In recent years, a hardware-accelerated version of AutoDock, called AutoDock-GPU, has been under active development. This work benchmarks the recent code and algorithmic enhancements incorporated into AutoDock-GPU. Particularly, we analyze the impact on execution runtime of techniques based on early termination. These enable AutoDock-GPU to explore the molecular space as necessary, while safely avoiding redundant computations.

SUBMITTER: Solis-Vasquez L 

PROVIDER: S-EPMC8654209 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature