Table 3.
Docking protocols, search algorithms, and scoring functions considered in this study.
| Score | Search Algorithm | Scoring Function | Protocol Abbrv. |
|---|---|---|---|
| Autodock 4.2 | Local search | Autodock SF | autodock-ls |
| Lamarckian GA | autodock-lga | ||
| GA | autodock-ga | ||
| Glide 6.5 | Glide algorithm | Standard precision | glide-sp |
| GOLD 5.4.1 | GA | ASP | gold-asp |
| Chemscore | gold-chemscore | ||
| Goldscore | gold-goldscore | ||
| PLP | gold-plp | ||
| PLANTS 1.2 | ACO algorithm | ChemPLP | plants-chemplp |
| PLP | plants-plp | ||
| PLP95 | plants-plp95 | ||
| rDock 2013.1 | GA + MC + Simplex minimization | rDock master SF | rdock-std |
| rDock master SF + desolvation | rdock-solv | ||
| Vina 1.1.2 | MC + BFGS local search | Vina SF | vina-std |
GA (Genetic Algorithm), MC (Monte Carlo), BFGS (Broyden–Fletcher–Goldfarb–Shanno), ASP (Astex Statistical Potential), PLP (Pairwise Linear Potential), ACO (Ant Colony Optimization).