Solis-Vasquez, Leonardo ; Koch, Andreas (2017)
A Performance and Energy Evaluation of OpenCL-Accelerated Molecular Docking.
5th International Workshop on OpenCL (IWOCL 2017). Toronto, Canada (16.05.2017-18.05.2017)
doi: 10.1145/3078155.3078167
Konferenzveröffentlichung, Bibliographie
Kurzbeschreibung (Abstract)
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.
| Typ des Eintrags: | Konferenzveröffentlichung |
|---|---|
| Erschienen: | 2017 |
| Autor(en): | Solis-Vasquez, Leonardo ; Koch, Andreas |
| Art des Eintrags: | Bibliographie |
| Titel: | A Performance and Energy Evaluation of OpenCL-Accelerated Molecular Docking |
| Sprache: | Englisch |
| Publikationsjahr: | 2017 |
| Verlag: | Association for Computing Machinery |
| Veranstaltungstitel: | 5th International Workshop on OpenCL (IWOCL 2017) |
| Veranstaltungsort: | Toronto, Canada |
| Veranstaltungsdatum: | 16.05.2017-18.05.2017 |
| DOI: | 10.1145/3078155.3078167 |
| Kurzbeschreibung (Abstract): | 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. |
| Freie Schlagworte: | AutoDock, energy efficiency, Molecular docking, parallelization, GPU, OpenCL |
| Zusätzliche Informationen: | Art. No.: 3 |
| Fachbereich(e)/-gebiet(e): | 20 Fachbereich Informatik 20 Fachbereich Informatik > Eingebettete Systeme und ihre Anwendungen |
| Hinterlegungsdatum: | 23 Nov 2020 10:31 |
| Letzte Änderung: | 23 Nov 2020 10:31 |
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