Fig 4.
(A) Bound reference structure of the protein homodimer test case (receptor, chain A of pdb2oo9, as blue and ligand protein, chain B of pdb2oo9, as pink cartoon) and random starting placements of the ligand protein around the receptor (different colors of cartoons). (B) Sampled RMSDlig during 10 MD simulations (same number as replicas used in the RP-REMD-Dock simulation) starting from the second start placement of the ligand protein. Each docking MD run was performed for 20 ns and results were concatenated for clarity to form a trajectory of 10x20ns = 200 ns resulting in a single overview plot (B). The sampled The RMSDlig of the reference replica during RP-REMD-Dock simulations starting from the same initial placement as used in the MD simulations is illustrated in (C).