Table 5.
GPU-powered tools to predict molecular structures, along with the speed-up achieved and the solutions used for code parallelization
| Prediction and searching of molecular structures | ||||
|---|---|---|---|---|
| Tool name | Speed-up | Parallel solution | Reference | |
| RNA secondary structure with dynamic programming | – | 17× | GPU | [89] |
| RNA secondary structure with Zucker algorithm | – | 6.75–15.93× | CPU-GPU | [92] |
| Molecular distance geometry problem with a memetic algorithm | memHPG | – | CPU-GPU | [93] |
| Protein alignment | GPU-CASSERT | 180× | GPU | [96] |
| Protein alignment based on Simulated Annealing | – | – | GPU | [97] |