Table 3. RMSD (Å) with respect to native pose before and after molecular docking.

The predicted conformations from the simulations with flexible side-chain constraints are used as initial conformations for docking calculations. We report the lowest RMSD values from the top five lowest energy conformations and their rank in predicted models predicted by MedusaDock and FlexPepDock. We also compare our results with castP and PEPSITE server (see Table S5).

PDB ID	Initial	MedusaDock	FlexPepDock
1BFE	2.51	2.85 (2)	2.49 (4)
1DDW	7.14	5.98 (5)	6.83 (3)
1CL5	8.27	3.73 (4)	7.42 (1)
2HPJ	3.26	5.05 (2)	3.02 (1)
1X2J	10.51	8.33 (4)	9.56 (4)
1SRL	7.73	5.71 (4)	6.83 (3)
2ID8	9.59	6.70 (1)	9.80 (3)