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. Author manuscript; available in PMC: 2021 Sep 8.
Published in final edited form as: J Chem Theory Comput. 2020 Aug 12;16(9):5512–5525. doi: 10.1021/acs.jctc.0c00237

Figure 2:

Figure 2:

RBFE results for PTP1B ligands:

Upper panels: simulations results with the original AMBER softcore potential parameter set and the linear combination of the softcore potentials, analyzed by TI (left panels) and MBAR (right panels).

Lower panels: simulations results with the proposed second order smoothstep function SSC(2) and the softcore potential parameter set (α=0.2, β=50 Å2), analyzed by TI (left panels) and MBAR (right panels). Plots show the the comparison between the stepwise scheme (x-axis) and the concerted scheme (y-axis). The dashed red lines indicate the region of ±1.0 kcal/mol difference. The calculated ∣ϵ∣’s are positive definite values and not normally distributed, hence their standard deviations (shown in parentheses) should not be interpretted as indicative of data range.