Table 3.

Results of FEP+ and TIES‐λ‐REST(‐MBAR) with different numbers of replicas and simulation lengths. Standard deviations in parentheses

Protein	Property	FEP+			TIES‐λ‐REST			TIES‐λ‐REST‐MBAR
		4 ns 5 reps	4 ns 30 reps	40 ns 20 reps	4 ns 5 reps	4 ns 20 reps	40 ns 10 reps	4 ns 5 reps	4 ns 20 reps	40 ns 10 reps
BRD4 MCL1 TYK2	No. of pert.	15
	MUE	0.96 (0.21)	0.91 (0.18)	1.04 (0.22)	0.97 (0.28)	0.96 (0.27)	0.92 (0.23)	0.86 (0.28)	0.89 (0.26)	0.89 (0.23)
	MSE	−0.13 (0.35)	−0.13 (0.32)	−0.65 (0.33)	−0.15 (0.40)	−0.03 (0.40)	−0.16 (0.36)	−0.22 (0.38)	−0.12 (0.38)	−0.25 (0.24)
	RMSE	1.21 (0.26)	1.10 (0.21)	1.33 (0.25)	1.40 (0.39)	1.32 (0.35)	1.23 (0.27)	1.33 (0.39)	1.28 (0.36)	1.19 (0.27)
	Correlation	0.87	0.89	0.78	0.77	0.79	0.79	0.78	0.80	0.80
	Slope	1.01	1.00	0.69	0.87	0.91	0.81	0.85	0.87	0.77
	intercept	0.52	0.52	−0.48	−0.02	0.03	−0.03	0.12	0.17	0.08