Figure 7

Docking a large ligand using DINC. Given a protein (in yellow color), a ligand (in purple color), and the approximate location of binding site (encompassed by the box), DINC docks the ligand incrementally. The protein and the ligand shown in this figure are derived from the structure of the protein-ligand complex deposited in the PDB with ID 2FDP. An initial fragment of the ligand is selected such that it has 6 rotatable bonds. The fragment is docked and 5 docked conformations are selected. These conformations are extended by adding 3 more bonds and atoms that are directly rotated by the 3 bonds. The extended conformations are docked, 5 of the docked conformations are selected and are then extended. This is repeated until the ligand is fully docked. As also shown in Figure 1, the docked conformation of the ligand is spatially close to the true conformation. For clarity, only one of the 5 selected conformations is shown at each step.