Fig 6.
(A) Initial Placement of the DNA minor groove binding ligand BFR at the center of a dsDNA molecule (cyan stick model, the guanine:cytosine base pairs are shown in white:green and the adeneine:thymine in pink cyan color coding, respectively). Hydrogen atoms, explicit waters and ions are omitted for clarity. (B) Superposition of sampled ligand snapshots (75 stick models) obtained from MD simulation and (C) same number of snapshots observed during RP-REMD-Dock in the reference replica. Sampled RMSDlig observed in four example MD simulations (color coded lines in D) and in the REMD reference replica (E). The discrete RMSDlig states are indicated by arrows. (F-J) Snapshots representing clusters of minor groove ligand binding states sampled during RP-REMD-Dock along the DNA minor groove.