Table 7:
Relative binding free energy values (kcal/mol) for four alchemical transformation pathways/softcore potentials
| Transformation | S0[6, 2, 0.5, 12] | S0[6, 2, 0.2, 17.3] | S2[6, 2, 0.2, 50] | S2*[2, 2, 0.5, 1] | Ref. |
|---|---|---|---|---|---|
| L66→L75 | −0.72(09) | −0.77(12) | −0.82(09) | −0.69(17) | −0.84(05) |
| L67→L66 | 0.83(05) | 0.75(06) | 0.78(05) | 0.72(05) | 0.74(03) |
| L67→L74 | −0.24(26) | −0.17(18) | −0.04(12) | 0.15(10) | −0.08(06) |
| L67→L75 | −0.32(28) | −0.17(14) | −0.12(09) | −0.05(13) | −0.06(05) |
| L74→L66 | 0.77(08) | 0.84(19) | 0.92(14) | 0.81(16) | 0.88(06) |
| L74→L75 | 0.19(15) | −0.27(51) | 0.01(16) | 0.21(14) | 0.01(06) |
| MUE | 0.15 | 0.10 | 0.03 | 0.11 | |
| RMSE | 0.15 | 0.12 | 0.04 | 0.13 |
a
Relative binding free energy values are obtained by concerted scheme and analyzed using the TI method. Standard errors are shown in parentheses (multiplied by 102). Accurate reference values (Ref.) were obtained from ACES calculations, sampled with 16 independent trials (as opposed to 4 for other calculations) and 25 A windows (as opposed to 21 for other calculations), and analyzed with BAR method (see Methods section 3.4 for details).