Fig 1.
Cartoon representation of the two domains of NS5 protein of dengue virus chosen as a target structure.
Table 1.
List of flavonoids with binding affinities from molecular docking calculations.
Fig 2.
2D projection of interaction of ligands with protein.
(a) FLD1 (b) FLD2 (c) FLD3 (d) FLD4, and (e) FLD5.
Fig 3.
RMSD of (a) ligands relative to protein backbone and (b) protein backbones relative to protein backbone, (c) RMSF curves of α-carbon atoms of protein, (d) Rg curves of protein, and (e) SASA of protein in different complexes obtained from 200 ns MDS trajectories Adducts with flavonoids; Indigo curve = FLD1, red curve = FLD2, blue curve = FLD3, maroon curve = FLD4, green curve = FLD5.
Table 2.
Different types of interaction and key amino acid residues of protein (PDB ID 5ZQK) in different complexes.
Fig 4.
Number of hydrogen bonds between protein and ligands in different complexes monitored during 200 ns production runs.
Adducts with flavonoids; Indigo line = FLD1, red line = FLD2, blue line = FLD3, maroon line = FLD4, green line = FLD5.
Fig 5.
The radial pair distribution function of the ligand and protein in five different complexes extracted from MDS trajectory.
(a) FLD1, (b) FLD2, (c) FLD3, (d) FLD4, and (e) FLD5; a sharp single peak indicates the localization of the ligand at a definite site in the protein pointing towards the spatial stability of the adduct.
Table 3.
Change in binding free energies (kcal/mol) of complexes with different components.