Table 3.

Summary of the MD simulation replicas 1 and 2 of DENV2, YFVm and WNV NS2B/NS3^pro in complex (with HST and HSD molecules).

Protein + Ligand	Replicate	Binding Energy [kcal/mol]	Representative Frames Cluster [%]
DENV2 NS2B/NS3pro–HST	1	−23.1 ± 3.6	68.9
	2	−24.1 ± 3.7	62.0
YFV NS2B/NS3pro–HST	1	−20.0 ± 3.4	54.9
	2	−19.4 ± 2.7	64.8
WNV NS2B/NS3pro–HST	1	−20.2 ± 3.4	72.7
	2	−28.3 ± 3.0	90.3
DENV2 NS2B/NS3pro–HSD	1	−37.4 ± 7.2	95.3
	2	−38.6 ± 8.0	75.0
YFV NS2B/NS3pro–HSD	1	−35.4 ± 5.2	36.9
	2	−37.6 ± 6.2	75.7
WNV NS2B/NS3pro–HSD	1	−40.7 ± 4.7	63.1
	2	−37.8 ± 7.0	54.2

Chosen representative protease–ligand structure in bold.