Figure 1
Pseudocode for the inverse docking workflow.
Table 1
Performance of Crossflow for the SWISH workflow [16], compared to the standard AMBER (multipmemd) reference implementation.
| CODE | PLATFORM | WALLCLOCK TIME (S – MEAN OF DUPLICATE RUNS) | SPEEDUP |
|---|---|---|---|
multipmemd | 64 CPU cores | 272 | – |
multipmemd | 128 CPU cores | 145 | |
pmemd.cuda + crossflow | 1 GPU | 229 | 1.00 |
pmemd.cuda + crossflow | 2 GPUs | 118 | 1.94 |
pmemd.cuda + crossflow | 4 GPUs | 62 | 3.69 |
pmemd.cuda + crossflow | 8 GPUs | 35 | 6.54 |
Table 2
Scaling performance of a Weighted Ensemble workflow. A “segment” is a short MD simulation of one member of the ensemble.
| NUMBER OF WORKERS | PERFORMANCE | MEAN WALLCLOCK TIME PER SEGMENT (SECONDS) | SPEEDUP |
|---|---|---|---|
| 1 | 280 segments in 1154.8 seconds | 4.12 | 1 |
| 2 | 384 segments in 936.3 seconds | 2.44 | 1.7 |
| 4 | 484 segments in 699.6 seconds | 1.45 | 2.8 |
| 8 | 424 segments in 397.9 seconds | 0.94 | 4.4 |
| 16 | 220 segments in 118.5 seconds | 0.54 | 7.6 |
Figure 2
Scores for ligand PRZ docked to 81 different protein targets (higher rank = better score). The score for the established binding partner (MUP, PDB code 1QY1) is indicated by the orange dot.