Table 4.
Values of Vina score, calculated GROMACS total-energy, and calculated binding free energies using MMPBSA (kJ/mol) of loop and hairpin region truncated from each aptamer. H02a gives the lowest MMPBSA ∆E binding energy compared to other complexes.
| Aptamer | Binding energy | ||
|---|---|---|---|
| Vina score (kJ/mol) | GROMACS Total energy (kJ/mol) | MM/PBSA ∆E binding (kJ/mol) | |
| H01a | -27.196 | -6.32094 x 105 | -971.119 |
| H01b | -31.798 | -7.73169 x 105 | -977.181 |
| H02a | -24.686 | -7.73238 x 105 | -1303.080 |
| H02b | -24.686 | -7.93305 x 105 | -974.453 |
| H03a | -22.175 | -7.71841 x 105 | -762.144 |