Fig 2. The artificial “homeodomain” test case consists of a single ligand helix (light blue cartoon) that corresponds to the third helix of 3rdhomeodomain from human homeoz protein (pdb2sy9) whereas the receptor was formed by the remaining helix 1 and 2 segments (dark blue cartoon).
The loop segment between helix 2 and helix 3 in the original structure was eliminated to yield a complex of two peptide molecules. For the MD simulations the ligand helix was initially placed on the opposite site of the native placement and snapshots of sampled states after 20, 200, 800 and 1500 ps are indicated (red cartoon). The upper panels indicate snapshots obtained during regular MD simulation. Lower panels are snapshots found in the RP-REMD-Dock reference replica. At the final stage sampling (last panel on the right) several of the sampled configurations overlap with the native placement of the helix 3 ligand as found in the original homeodomain structure.